diff --git a/404.html b/404.html index 4cfd25d..f27a1c2 100644 --- a/404.html +++ b/404.html @@ -18,7 +18,7 @@ - +
@@ -47,7 +47,7 @@
  • @@ -78,7 +78,7 @@
    • - +
    @@ -101,21 +101,21 @@

    Page not found (404)

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/articles/EpiCompare.html b/articles/EpiCompare.html index dcb8bce..7cd8bfd 100644 --- a/articles/EpiCompare.html +++ b/articles/EpiCompare.html @@ -12,14 +12,13 @@ - - +
    @@ -48,7 +47,7 @@
  • @@ -79,7 +78,7 @@
    • - +
    @@ -89,15 +88,15 @@


    Authors: Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, -Nathan Skene, Thomas Roberts
    +Nathan Skene, Thomas Roberts, Hiranyamaya Dash


    -Vignette updated: Apr-25-2024
    +Vignette updated: Oct-18-2024

    - Source: vignettes/EpiCompare.Rmd + Source: vignettes/EpiCompare.Rmd
    @@ -317,12 +316,12 @@

    Run EpiCompare## - add_download_button= 
    ## processing file: EpiCompare.Rmd
    ## output file: EpiCompare.knit.md
    -
    ## /usr/local/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpePHAFz/EpiCompare_test.html --lua-filter /__w/_temp/Library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /__w/_temp/Library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /__w/_temp/Library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css custom.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpePHAFz/rmarkdown-str8b4527b8e24d.html --variable code_folding=hide --variable code_menu=1
    +
    ## /usr/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp6sR0mw/EpiCompare_test.html --lua-filter /__w/_temp/Library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /__w/_temp/Library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /__w/_temp/Library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /__w/_temp/Library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css custom.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp6sR0mw/rmarkdown-str4cd753601da.html --variable code_folding=hide --variable code_menu=1
    ## 
-## Output created: /tmp/RtmpePHAFz/EpiCompare_test.html
    +## Output created: /tmp/Rtmp6sR0mw/EpiCompare_test.html 
    ## [1] "Done in 0.11 min."
    -
    ## All outputs saved to: /tmp/RtmpePHAFz
    -
    ## [1] "/tmp/RtmpePHAFz/EpiCompare_test.html"
    +
    ## All outputs saved to: /tmp/Rtmp6sR0mw
    +
    ## [1] "/tmp/Rtmp6sR0mw/EpiCompare_test.html"

    Optional plots

    @@ -487,9 +486,9 @@

    Session Information
     utils::sessionInfo()

    -
    ## R version 4.4.0 RC (2024-04-16 r86441)
+
    ## R version 4.4.1 (2024-06-14)
 ## Platform: x86_64-pc-linux-gnu
-## Running under: Ubuntu 22.04.4 LTS
+## Running under: Ubuntu 22.04.5 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -510,190 +509,187 @@ 
    Session Information## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] EpiCompare_1.7.5 BiocStyle_2.31.0
+## [1] EpiCompare_1.9.10 BiocStyle_2.33.1 
 ## 
 ## loaded via a namespace (and not attached):
-##   [1] splines_4.4.0                          
-##   [2] BiocIO_1.13.0                          
-##   [3] bitops_1.0-7                           
+##   [1] splines_4.4.1                          
+##   [2] BiocIO_1.15.2                          
+##   [3] bitops_1.0-9                           
 ##   [4] ggplotify_0.1.2                        
 ##   [5] filelock_1.0.3                         
 ##   [6] tibble_3.2.1                           
-##   [7] polyclip_1.10-6                        
-##   [8] XML_3.99-0.16.1                        
-##   [9] lifecycle_1.0.4                        
-##  [10] lattice_0.22-6                         
-##  [11] MASS_7.3-60.2                          
-##  [12] magrittr_2.0.3                         
-##  [13] plotly_4.10.4                          
-##  [14] sass_0.4.9                             
-##  [15] rmarkdown_2.26                         
-##  [16] jquerylib_0.1.4                        
-##  [17] yaml_2.3.8                             
-##  [18] BRGenomics_1.15.0                      
+##   [7] R.oo_1.26.0                            
+##   [8] polyclip_1.10-7                        
+##   [9] XML_3.99-0.17                          
+##  [10] lifecycle_1.0.4                        
+##  [11] lattice_0.22-6                         
+##  [12] MASS_7.3-61                            
+##  [13] magrittr_2.0.3                         
+##  [14] plotly_4.10.4                          
+##  [15] sass_0.4.9                             
+##  [16] rmarkdown_2.28                         
+##  [17] jquerylib_0.1.4                        
+##  [18] yaml_2.3.10                            
 ##  [19] plotrix_3.8-4                          
 ##  [20] cowplot_1.1.3                          
-##  [21] DBI_1.2.2                              
+##  [21] DBI_1.2.3                              
 ##  [22] RColorBrewer_1.1-3                     
 ##  [23] lubridate_1.9.3                        
-##  [24] abind_1.4-5                            
-##  [25] zlibbioc_1.49.3                        
-##  [26] GenomicRanges_1.55.4                   
+##  [24] abind_1.4-8                            
+##  [25] zlibbioc_1.51.1                        
+##  [26] GenomicRanges_1.57.2                   
 ##  [27] purrr_1.0.2                            
-##  [28] ggraph_2.2.1                           
-##  [29] BiocGenerics_0.49.1                    
-##  [30] RCurl_1.98-1.14                        
-##  [31] yulab.utils_0.1.4                      
-##  [32] tweenr_2.0.3                           
-##  [33] rappdirs_0.3.3                         
-##  [34] GenomeInfoDbData_1.2.12                
-##  [35] IRanges_2.37.1                         
-##  [36] S4Vectors_0.41.7                       
-##  [37] enrichplot_1.23.2                      
-##  [38] ggrepel_0.9.5                          
-##  [39] tidytree_0.4.6                         
-##  [40] pkgdown_2.0.9                          
-##  [41] ChIPseeker_1.39.0                      
-##  [42] codetools_0.2-20                       
-##  [43] DelayedArray_0.29.9                    
-##  [44] DOSE_3.29.2                            
-##  [45] ggforce_0.4.2                          
-##  [46] tidyselect_1.2.1                       
-##  [47] aplot_0.2.2                            
-##  [48] UCSC.utils_0.99.7                      
-##  [49] farver_2.1.1                           
-##  [50] viridis_0.6.5                          
-##  [51] base64enc_0.1-3                        
-##  [52] matrixStats_1.3.0                      
-##  [53] stats4_4.4.0                           
-##  [54] BiocFileCache_2.11.2                   
-##  [55] GenomicAlignments_1.39.5               
-##  [56] jsonlite_1.8.8                         
+##  [28] R.utils_2.12.3                         
+##  [29] ggraph_2.2.1                           
+##  [30] BiocGenerics_0.51.3                    
+##  [31] RCurl_1.98-1.16                        
+##  [32] yulab.utils_0.1.7                      
+##  [33] tweenr_2.0.3                           
+##  [34] rappdirs_0.3.3                         
+##  [35] GenomeInfoDbData_1.2.13                
+##  [36] IRanges_2.39.2                         
+##  [37] S4Vectors_0.43.2                       
+##  [38] enrichplot_1.25.3                      
+##  [39] ggrepel_0.9.6                          
+##  [40] tidytree_0.4.6                         
+##  [41] pkgdown_2.1.1                          
+##  [42] ChIPseeker_1.41.3                      
+##  [43] codetools_0.2-20                       
+##  [44] DelayedArray_0.31.14                   
+##  [45] DOSE_3.99.1                            
+##  [46] ggforce_0.4.2                          
+##  [47] tidyselect_1.2.1                       
+##  [48] aplot_0.2.3                            
+##  [49] UCSC.utils_1.1.0                       
+##  [50] farver_2.1.2                           
+##  [51] viridis_0.6.5                          
+##  [52] matrixStats_1.4.1                      
+##  [53] stats4_4.4.1                           
+##  [54] BiocFileCache_2.13.2                   
+##  [55] GenomicAlignments_1.41.0               
+##  [56] jsonlite_1.8.9                         
 ##  [57] tidygraph_1.3.1                        
-##  [58] systemfonts_1.0.6                      
-##  [59] tools_4.4.0                            
-##  [60] treeio_1.27.1                          
+##  [58] systemfonts_1.1.0                      
+##  [59] tools_4.4.1                            
+##  [60] treeio_1.29.1                          
 ##  [61] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
-##  [62] ragg_1.3.0                             
-##  [63] Rcpp_1.0.12                            
-##  [64] glue_1.7.0                             
+##  [62] ragg_1.3.3                             
+##  [63] Rcpp_1.0.13                            
+##  [64] glue_1.8.0                             
 ##  [65] gridExtra_2.3                          
-##  [66] SparseArray_1.3.5                      
-##  [67] xfun_0.43                              
-##  [68] DESeq2_1.43.5                          
-##  [69] qvalue_2.35.0                          
-##  [70] MatrixGenerics_1.15.1                  
-##  [71] GenomeInfoDb_1.39.14                   
-##  [72] dplyr_1.1.4                            
-##  [73] withr_3.0.0                            
-##  [74] BiocManager_1.30.22                    
-##  [75] fastmap_1.1.1                          
-##  [76] boot_1.3-30                            
-##  [77] fansi_1.0.6                            
-##  [78] caTools_1.18.2                         
-##  [79] digest_0.6.35                          
-##  [80] mime_0.12                              
-##  [81] timechange_0.3.0                       
-##  [82] R6_2.5.1                               
-##  [83] gridGraphics_0.5-1                     
-##  [84] seqPattern_1.35.0                      
-##  [85] textshaping_0.3.7                      
-##  [86] colorspace_2.1-0                       
-##  [87] GO.db_3.19.1                           
-##  [88] gtools_3.9.5                           
-##  [89] RSQLite_2.3.6                          
-##  [90] utf8_1.2.4                             
-##  [91] tidyr_1.3.1                            
-##  [92] generics_0.1.3                         
-##  [93] data.table_1.15.4                      
-##  [94] bsplus_0.1.4                           
-##  [95] rtracklayer_1.63.2                     
-##  [96] graphlayouts_1.1.1                     
-##  [97] httr_1.4.7                             
-##  [98] htmlwidgets_1.6.4                      
-##  [99] S4Arrays_1.3.7                         
-## [100] scatterpie_0.2.2                       
-## [101] downloadthis_0.3.3                     
-## [102] pkgconfig_2.0.3                        
-## [103] gtable_0.3.5                           
-## [104] blob_1.2.4                             
-## [105] impute_1.77.0                          
-## [106] XVector_0.43.1                         
-## [107] shadowtext_0.1.3                       
-## [108] htmltools_0.5.8.1                      
-## [109] bookdown_0.39                          
-## [110] fgsea_1.29.2                           
-## [111] scales_1.3.0                           
-## [112] Biobase_2.63.1                         
-## [113] png_0.1-8                              
-## [114] ggfun_0.1.4                            
-## [115] knitr_1.46                             
-## [116] tzdb_0.4.0                             
-## [117] reshape2_1.4.4                         
-## [118] rjson_0.2.21                           
-## [119] nlme_3.1-164                           
-## [120] curl_5.2.1                             
-## [121] cachem_1.0.8                           
-## [122] stringr_1.5.1                          
-## [123] BiocVersion_3.19.1                     
-## [124] KernSmooth_2.23-22                     
-## [125] parallel_4.4.0                         
-## [126] HDO.db_0.99.1                          
-## [127] AnnotationDbi_1.65.2                   
+##  [66] SparseArray_1.5.44                     
+##  [67] xfun_0.48                              
+##  [68] qvalue_2.37.0                          
+##  [69] MatrixGenerics_1.17.0                  
+##  [70] GenomeInfoDb_1.41.2                    
+##  [71] dplyr_1.1.4                            
+##  [72] withr_3.0.1                            
+##  [73] BiocManager_1.30.25                    
+##  [74] fastmap_1.2.0                          
+##  [75] boot_1.3-31                            
+##  [76] fansi_1.0.6                            
+##  [77] caTools_1.18.3                         
+##  [78] digest_0.6.37                          
+##  [79] mime_0.12                              
+##  [80] timechange_0.3.0                       
+##  [81] R6_2.5.1                               
+##  [82] gridGraphics_0.5-1                     
+##  [83] seqPattern_1.37.0                      
+##  [84] textshaping_0.4.0                      
+##  [85] colorspace_2.1-1                       
+##  [86] GO.db_3.20.0                           
+##  [87] gtools_3.9.5                           
+##  [88] RSQLite_2.3.7                          
+##  [89] b64_0.1.3                              
+##  [90] R.methodsS3_1.8.2                      
+##  [91] utf8_1.2.4                             
+##  [92] tidyr_1.3.1                            
+##  [93] generics_0.1.3                         
+##  [94] data.table_1.16.2                      
+##  [95] bsplus_0.1.4                           
+##  [96] rtracklayer_1.65.0                     
+##  [97] graphlayouts_1.2.0                     
+##  [98] httr_1.4.7                             
+##  [99] htmlwidgets_1.6.4                      
+## [100] S4Arrays_1.5.11                        
+## [101] scatterpie_0.2.4                       
+## [102] downloadthis_0.4.1                     
+## [103] pkgconfig_2.0.3                        
+## [104] gtable_0.3.5                           
+## [105] blob_1.2.4                             
+## [106] impute_1.79.0                          
+## [107] XVector_0.45.0                         
+## [108] shadowtext_0.1.4                       
+## [109] htmltools_0.5.8.1                      
+## [110] bookdown_0.41                          
+## [111] fgsea_1.31.6                           
+## [112] scales_1.3.0                           
+## [113] Biobase_2.65.1                         
+## [114] png_0.1-8                              
+## [115] ggfun_0.1.6                            
+## [116] knitr_1.48                             
+## [117] tzdb_0.4.0                             
+## [118] reshape2_1.4.4                         
+## [119] rjson_0.2.23                           
+## [120] nlme_3.1-166                           
+## [121] curl_5.2.3                             
+## [122] cachem_1.1.0                           
+## [123] stringr_1.5.1                          
+## [124] BiocVersion_3.20.0                     
+## [125] KernSmooth_2.23-24                     
+## [126] parallel_4.4.1                         
+## [127] AnnotationDbi_1.67.0                   
 ## [128] restfulr_0.0.15                        
 ## [129] desc_1.4.3                             
 ## [130] pillar_1.9.0                           
-## [131] grid_4.4.0                             
+## [131] grid_4.4.1                             
 ## [132] vctrs_0.6.5                            
-## [133] gplots_3.1.3.1                         
+## [133] gplots_3.2.0                           
 ## [134] dbplyr_2.5.0                           
-## [135] evaluate_0.23                          
+## [135] evaluate_1.0.1                         
 ## [136] readr_2.1.5                            
-## [137] GenomicFeatures_1.55.4                 
-## [138] cli_3.6.2                              
-## [139] locfit_1.5-9.9                         
-## [140] compiler_4.4.0                         
-## [141] Rsamtools_2.19.4                       
-## [142] rlang_1.1.3                            
-## [143] crayon_1.5.2                           
-## [144] labeling_0.4.3                         
-## [145] plyr_1.8.9                             
-## [146] fs_1.6.4                               
-## [147] stringi_1.8.3                          
-## [148] genomation_1.35.0                      
-## [149] viridisLite_0.4.2                      
-## [150] gridBase_0.4-7                         
-## [151] BiocParallel_1.37.1                    
-## [152] munsell_0.5.1                          
-## [153] Biostrings_2.71.6                      
-## [154] lazyeval_0.2.2                         
-## [155] GOSemSim_2.29.2                        
-## [156] Matrix_1.7-0                           
-## [157] BSgenome_1.71.4                        
-## [158] hms_1.1.3                              
-## [159] patchwork_1.2.0                        
-## [160] bit64_4.0.5                            
-## [161] ggplot2_3.5.1                          
-## [162] KEGGREST_1.43.0                        
-## [163] highr_0.10                             
-## [164] SummarizedExperiment_1.33.3            
-## [165] AnnotationHub_3.11.5                   
-## [166] igraph_2.0.3                           
-## [167] memoise_2.0.1                          
-## [168] bslib_0.7.0                            
-## [169] ggtree_3.11.2                          
-## [170] fastmatch_1.1-4                        
-## [171] bit_4.0.5                              
-## [172] ape_5.8
    
+## [137] GenomicFeatures_1.57.1                 
+## [138] cli_3.6.3                              
+## [139] compiler_4.4.1                         
+## [140] Rsamtools_2.21.2                       
+## [141] rlang_1.1.4                            
+## [142] crayon_1.5.3                           
+## [143] labeling_0.4.3                         
+## [144] plyr_1.8.9                             
+## [145] fs_1.6.4                               
+## [146] stringi_1.8.4                          
+## [147] genomation_1.37.0                      
+## [148] viridisLite_0.4.2                      
+## [149] gridBase_0.4-7                         
+## [150] BiocParallel_1.39.0                    
+## [151] munsell_0.5.1                          
+## [152] Biostrings_2.73.2                      
+## [153] lazyeval_0.2.2                         
+## [154] GOSemSim_2.31.2                        
+## [155] Matrix_1.7-0                           
+## [156] BSgenome_1.73.1                        
+## [157] hms_1.1.3                              
+## [158] patchwork_1.3.0                        
+## [159] bit64_4.5.2                            
+## [160] ggplot2_3.5.1                          
+## [161] KEGGREST_1.45.1                        
+## [162] highr_0.11                             
+## [163] SummarizedExperiment_1.35.4            
+## [164] AnnotationHub_3.13.3                   
+## [165] igraph_2.0.3                           
+## [166] memoise_2.0.1                          
+## [167] bslib_0.8.0                            
+## [168] ggtree_3.13.1                          
+## [169] fastmatch_1.1-4                        
+## [170] bit_4.5.0                              
+## [171] ape_5.8

    + @@ -701,21 +697,21 @@

    Session Information

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/articles/docker.html b/articles/docker.html index 6d5f68c..0a79bbd 100644 --- a/articles/docker.html +++ b/articles/docker.html @@ -12,14 +12,13 @@ - - +
    @@ -48,7 +47,7 @@
  • @@ -79,7 +78,7 @@
    • - +
    @@ -88,15 +87,15 @@

    Docker/Singularity Containers


    Authors: Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, -Nathan Skene, Thomas Roberts
    +Nathan Skene, Thomas Roberts, Hiranyamaya Dash


    -Vignette updated: Apr-25-2024
    +Vignette updated: Oct-18-2024

    - Source: vignettes/docker.Rmd + Source: vignettes/docker.Rmd @@ -171,9 +170,9 @@

    Session Info
     utils::sessionInfo()
    -
    ## R version 4.4.0 RC (2024-04-16 r86441)
+
    ## R version 4.4.1 (2024-06-14)
 ## Platform: x86_64-pc-linux-gnu
-## Running under: Ubuntu 22.04.4 LTS
+## Running under: Ubuntu 22.04.5 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -194,183 +193,180 @@ 
    Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] EpiCompare_1.7.5 BiocStyle_2.31.0
+## [1] EpiCompare_1.9.10 BiocStyle_2.33.1 
 ## 
 ## loaded via a namespace (and not attached):
-##   [1] splines_4.4.0                          
-##   [2] BiocIO_1.13.0                          
-##   [3] bitops_1.0-7                           
+##   [1] splines_4.4.1                          
+##   [2] BiocIO_1.15.2                          
+##   [3] bitops_1.0-9                           
 ##   [4] ggplotify_0.1.2                        
 ##   [5] filelock_1.0.3                         
 ##   [6] tibble_3.2.1                           
-##   [7] polyclip_1.10-6                        
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 ##  [20] cowplot_1.1.3                          
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+##  [85] RSQLite_2.3.7                          
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+## [103] shadowtext_0.1.4                       
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+## [108] Biobase_2.65.1                         
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+## [112] tzdb_0.4.0                             
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+## [120] KernSmooth_2.23-24                     
+## [121] parallel_4.4.1                         
+## [122] AnnotationDbi_1.67.0                   
 ## [123] restfulr_0.0.15                        
 ## [124] desc_1.4.3                             
 ## [125] pillar_1.9.0                           
-## [126] grid_4.4.0                             
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 ## [127] vctrs_0.6.5                            
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+## [128] gplots_3.2.0                           
 ## [129] dbplyr_2.5.0                           
-## [130] evaluate_0.23                          
+## [130] evaluate_1.0.1                         
 ## [131] readr_2.1.5                            
-## [132] GenomicFeatures_1.55.4                 
-## [133] cli_3.6.2                              
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-## [149] GOSemSim_2.29.2                        
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-## [151] BSgenome_1.71.4                        
-## [152] hms_1.1.3                              
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-## [154] bit64_4.0.5                            
-## [155] ggplot2_3.5.1                          
-## [156] KEGGREST_1.43.0                        
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-## [158] AnnotationHub_3.11.5                   
-## [159] igraph_2.0.3                           
-## [160] memoise_2.0.1                          
-## [161] bslib_0.7.0                            
-## [162] ggtree_3.11.2                          
-## [163] fastmatch_1.1-4                        
-## [164] bit_4.0.5                              
-## [165] ape_5.8
    
+## [132] GenomicFeatures_1.57.1                 
+## [133] cli_3.6.3                              
+## [134] compiler_4.4.1                         
+## [135] Rsamtools_2.21.2                       
+## [136] rlang_1.1.4                            
+## [137] crayon_1.5.3                           
+## [138] plyr_1.8.9                             
+## [139] fs_1.6.4                               
+## [140] stringi_1.8.4                          
+## [141] genomation_1.37.0                      
+## [142] viridisLite_0.4.2                      
+## [143] gridBase_0.4-7                         
+## [144] BiocParallel_1.39.0                    
+## [145] munsell_0.5.1                          
+## [146] Biostrings_2.73.2                      
+## [147] lazyeval_0.2.2                         
+## [148] GOSemSim_2.31.2                        
+## [149] Matrix_1.7-0                           
+## [150] BSgenome_1.73.1                        
+## [151] hms_1.1.3                              
+## [152] patchwork_1.3.0                        
+## [153] bit64_4.5.2                            
+## [154] ggplot2_3.5.1                          
+## [155] KEGGREST_1.45.1                        
+## [156] SummarizedExperiment_1.35.4            
+## [157] AnnotationHub_3.13.3                   
+## [158] igraph_2.0.3                           
+## [159] memoise_2.0.1                          
+## [160] bslib_0.8.0                            
+## [161] ggtree_3.13.1                          
+## [162] fastmatch_1.1-4                        
+## [163] bit_4.5.0                              
+## [164] ape_5.8


    + @@ -378,21 +374,21 @@

    Session Info

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/articles/example_report.html b/articles/example_report.html index 9c94d22..1df2c85 100644 --- a/articles/example_report.html +++ b/articles/example_report.html @@ -12,14 +12,13 @@ - - +
    @@ -48,7 +47,7 @@
  • @@ -79,7 +78,7 @@
    • - +
    @@ -88,15 +87,15 @@

    Example report


    Authors: Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, -Nathan Skene, Thomas Roberts
    +Nathan Skene, Thomas Roberts, Hiranyamaya Dash


    -Vignette updated: Apr-25-2024
    +Vignette updated: Oct-18-2024

    - Source: vignettes/example_report.Rmd + Source: vignettes/example_report.Rmd @@ -149,9 +148,9 @@

    Session Information
     utils::sessionInfo()
    -
    ## R version 4.4.0 RC (2024-04-16 r86441)
+
    ## R version 4.4.1 (2024-06-14)
 ## Platform: x86_64-pc-linux-gnu
-## Running under: Ubuntu 22.04.4 LTS
+## Running under: Ubuntu 22.04.5 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -172,29 +171,26 @@ 
    Session Information## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] BiocStyle_2.31.0
+## [1] BiocStyle_2.33.1
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] vctrs_0.6.5         cli_3.6.2           knitr_1.46         
-##  [4] rlang_1.1.3         xfun_0.43           purrr_1.0.2        
-##  [7] textshaping_0.3.7   jsonlite_1.8.8      htmltools_0.5.8.1  
-## [10] ragg_1.3.0          sass_0.4.9          rmarkdown_2.26     
-## [13] evaluate_0.23       jquerylib_0.1.4     fastmap_1.1.1      
-## [16] yaml_2.3.8          lifecycle_1.0.4     memoise_2.0.1      
-## [19] bookdown_0.39       BiocManager_1.30.22 compiler_4.4.0     
-## [22] fs_1.6.4            htmlwidgets_1.6.4   systemfonts_1.0.6  
-## [25] digest_0.6.35       R6_2.5.1            magrittr_2.0.3     
-## [28] bslib_0.7.0         tools_4.4.0         pkgdown_2.0.9      
-## [31] cachem_1.0.8        desc_1.4.3
    
+##  [1] digest_0.6.37       desc_1.4.3          R6_2.5.1           
+##  [4] bookdown_0.41       fastmap_1.2.0       xfun_0.48          
+##  [7] cachem_1.1.0        knitr_1.48          htmltools_0.5.8.1  
+## [10] rmarkdown_2.28      lifecycle_1.0.4     cli_3.6.3          
+## [13] sass_0.4.9          pkgdown_2.1.1       textshaping_0.4.0  
+## [16] jquerylib_0.1.4     systemfonts_1.1.0   compiler_4.4.1     
+## [19] tools_4.4.1         ragg_1.3.3          bslib_0.8.0        
+## [22] evaluate_1.0.1      yaml_2.3.10         BiocManager_1.30.25
+## [25] jsonlite_1.8.9      rlang_1.1.4         fs_1.6.4           
+## [28] htmlwidgets_1.6.4
    + @@ -202,21 +198,21 @@

    Session Information

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/articles/index.html b/articles/index.html index 158399e..bb1822b 100644 --- a/articles/index.html +++ b/articles/index.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -78,19 +78,19 @@

    All vignettes

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/authors.html b/authors.html index 5295783..d7bd3c7 100644 --- a/authors.html +++ b/authors.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -63,7 +63,7 @@

    Authors and Citation

    - +

    • Sera Choi. Author.

      @@ -73,7 +73,7 @@

      Authors and Citation

    • -

      Leyla Abbasova. Author. +

      Leyla Abbasova. Author.

    • @@ -85,20 +85,24 @@

      Authors and Citation

    • -

      Thomas Roberts. Maintainer. +

      Thomas Roberts. Contributor. +

      +
      • +
    • +

      Hiranyamaya Dash. Maintainer.

    Citation

    - Source: inst/CITATION + Source: inst/CITATION
    -

    EpiCompare: R package for the comparison and quality control of epigenomic peak files (2022) - Sera Choi, Brian M. Schilder, Leyla Abbasova, Alan E. Murphy, Nathan G. Skene, +

    EpiCompare: R package for the comparison and quality control of epigenomic peak files (2022) + Sera Choi, Brian M. Schilder, Leyla Abbasova, Alan E. Murphy, Nathan G. Skene, bioRxiv, 2022.07.22.501149; doi: https://doi.org/10.1101/2022.07.22.501149

    @Article{,
   title = {EpiCompare: R package for the comparison and quality control of epigenomic peak files},
@@ -115,19 +119,19 @@ 
    Citation
    
 
 
       
    
-  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.
    
+  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/index.html b/index.html
index f72a5de..cae9ee5 100644
--- a/index.html
+++ b/index.html
@@ -19,7 +19,7 @@
 
 
 
-    
+
 
     
    
       
    
 
@@ -48,7 +48,7 @@
 
  • 
   
   
@@ -79,7 +79,7 @@
 
    • 
 
 
-      
+
 
       
    
   
    
@@ -87,12 +87,12 @@
 
    
 
    ⚖EpiCompare⚖
    QC and Benchmarking of Epigenomic Datasets
 
    
-
       download License: GPL-3  
       
    R build status  

    
-Authors: Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts
+
       download License: GPL-3  
       
    R build status  

    
+Authors: Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts, Hiranyamaya Dash
 
 
    
 
    
-Updated: Apr-25-2024
+Updated: Oct-18-2024
 
 
    
 
    
@@ -366,9 +366,9 @@ 
    Session Info
     utils::sessionInfo()
    
-
    ## R version 4.4.0 RC (2024-04-16 r86441)
+
    ## R version 4.4.1 (2024-06-14)
 ## Platform: x86_64-pc-linux-gnu
-## Running under: Ubuntu 22.04.4 LTS
+## Running under: Ubuntu 22.04.5 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -389,25 +389,24 @@ 
    Session Info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] rmarkdown_2.26
+## [1] rmarkdown_2.28
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] gtable_0.3.5        jsonlite_1.8.8      renv_1.0.7         
-##  [4] dplyr_1.1.4         compiler_4.4.0      BiocManager_1.30.22
+##  [1] gtable_0.3.5        jsonlite_1.8.9      renv_1.0.11        
+##  [4] dplyr_1.1.4         compiler_4.4.1      BiocManager_1.30.25
 ##  [7] tidyselect_1.2.1    rvcheck_0.2.1       scales_1.3.0       
-## [10] yaml_2.3.8          fastmap_1.1.1       here_1.0.1         
+## [10] yaml_2.3.10         fastmap_1.2.0       here_1.0.1         
 ## [13] ggplot2_3.5.1       R6_2.5.1            generics_0.1.3     
-## [16] knitr_1.46          yulab.utils_0.1.4   tibble_3.2.1       
+## [16] knitr_1.48          yulab.utils_0.1.7   tibble_3.2.1       
 ## [19] desc_1.4.3          dlstats_0.1.7       rprojroot_2.0.4    
 ## [22] munsell_0.5.1       pillar_1.9.0        RColorBrewer_1.1-3 
-## [25] rlang_1.1.3         utf8_1.2.4          cachem_1.0.8       
-## [28] badger_0.2.3        xfun_0.43           fs_1.6.4           
-## [31] memoise_2.0.1       cli_3.6.2           magrittr_2.0.3     
-## [34] rworkflows_1.0.1    digest_0.6.35       grid_4.4.0         
-## [37] lifecycle_1.0.4     vctrs_0.6.5         data.table_1.15.4  
-## [40] evaluate_0.23       glue_1.7.0          fansi_1.0.6        
-## [43] colorspace_2.1-0    tools_4.4.0         pkgconfig_2.0.3    
-## [46] htmltools_0.5.8.1
    
+## [25] rlang_1.1.4         utf8_1.2.4          badger_0.2.4       
+## [28] xfun_0.48           fs_1.6.4            cli_3.6.3          
+## [31] magrittr_2.0.3      rworkflows_1.0.2    digest_0.6.37      
+## [34] grid_4.4.1          lifecycle_1.0.4     vctrs_0.6.5        
+## [37] evaluate_1.0.1      glue_1.8.0          data.table_1.16.2  
+## [40] fansi_1.0.6         colorspace_2.1-1    tools_4.4.1        
+## [43] pkgconfig_2.0.3     htmltools_0.5.8.1
    
 
    
 
    
 
@@ -447,7 +446,8 @@ 
    Developers
    
 
  • Leyla Abbasova 
     Author   
    • 
 
  • Alan Murphy 
     Author   
    • 
 
  • Nathan Skene 
     Author   
    • 
-
  • Thomas Roberts 
     Maintainer   
    • 
+
  • Hiranyamaya Dash 
     Maintainer   
    • 
+
  • More about authors...
    • 
 
 
 
@@ -459,21 +459,21 @@ 
    Developers
    
 
       
    
   
    
-
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.
    
+
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.
    
 
    
 
 
    
   
    
-
    Site built with pkgdown 2.0.9.
    
+
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
 
-  
 
 
-  
+
+
 
   
 
diff --git a/news/index.html b/news/index.html
index a088756..56bc888 100644
--- a/news/index.html
+++ b/news/index.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
     
    
       
    Changelog 
    
-      Source: NEWS.md
+      Source: NEWS.md
     
    
 
+    
    
+
    CHANGES IN VERSION 1.9.5
    
+
    
+
    New features
    
+
    • Remove the soon-to-be-deprecated BRGenomics dependency.
+
      • Port tidyChromosomes function to EpiCompare.
        • 
+
      • 
+
    
+
    
+
    Miscellaneous
    
+
    • Update maintainer details.
      • 
+
    
+
    
     
    
 
    CHANGES IN VERSION 1.3.4
    
 
    
@@ -570,19 +583,19 @@ 
    New Features
    
-  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.
    
+  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/pkgdown.yml b/pkgdown.yml
index 8f8600b..662e08f 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,9 +1,8 @@
-pandoc: 3.1.1
-pkgdown: 2.0.9
+pandoc: '3.4'
+pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   docker: docker.html
   EpiCompare: EpiCompare.html
   example_report: example_report.html
-last_built: 2024-04-25T16:05Z
-
+last_built: 2024-10-18T14:19Z
diff --git a/reference/CnR_H3K27ac.html b/reference/CnR_H3K27ac.html
index ba98088..c2d9081 100644
--- a/reference/CnR_H3K27ac.html
+++ b/reference/CnR_H3K27ac.html
@@ -9,7 +9,7 @@
 
 
 
-    
+
 
     
    
       
    
 
@@ -37,7 +37,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
     
    
     
    Example CUT&Run peak file
    
-    Source: R/data.R
+    Source: R/data.R
     
     
    
 
@@ -92,8 +92,8 @@ 
    Format
    
     
    Source
    
     
    The code to prepare the .Rda file from the raw peak file is:
    
 
    # sequences were directly downloaded from
- https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8581604 
    # and peaks (BED file) were generated by Leyla Abbasova 
-(Neurogenomics Lab, Imperial College London) 
    CnR_H3K27ac <- ChIPseeker::readPeakFile("path", as = "GRanges") 
    CnR_H3K27ac <- CnR_H3K27ac[seqnames(CnR_H3K27ac)== "chr1"] 
    my_label <- 
+ https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8581604 
    # and peaks (BED file) were generated by Leyla Abbasova
+(Neurogenomics Lab, Imperial College London) 
    CnR_H3K27ac <- ChIPseeker::readPeakFile("path", as = "GRanges") 
    CnR_H3K27ac <- CnR_H3K27ac[seqnames(CnR_H3K27ac)== "chr1"] 
    my_label <-
 c("name","score","strand","signalValue","pValue","qValue","peak")
    colnames(GenomicRanges::mcols(CnR_H3K27ac)) <- my_label 
    usethis::use_data(CnR_H3K27ac, overwrite = TRUE) 
    
     
    
 
@@ -105,19 +105,19 @@ 
    Source
    
 
 
       
    
-  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.
    
+  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/CnR_H3K27ac_picard.html b/reference/CnR_H3K27ac_picard.html
index 4557cbc..ef587e5 100644
--- a/reference/CnR_H3K27ac_picard.html
+++ b/reference/CnR_H3K27ac_picard.html
@@ -1,14 +1,14 @@
 
-Example Picard duplication metrics file 2 — CnR_H3K27ac_picard • EpiCompareExample Picard duplication metrics file 2 — CnR_H3K27ac_picard • EpiCompare
-    
+
 
     
    
       
    
 
@@ -36,7 +36,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Example Picard duplication metrics file 2
    
-    Source: R/data.R
+    Source: R/data.R
     
     
    
 
     
    
-    
    Duplication metrics output on CUT&Run H3K27ac file 
+    
    Duplication metrics output on CUT&Run H3K27ac file
 (sample accession: SRR8581604).
-Raw sequences were aligned to hg19 genome and after, 
+Raw sequences were aligned to hg19 genome and after,
 Picard was performed by Leyla Abbasova.
-The duplication summary output generated by Picard 
+The duplication summary output generated by Picard
 was processed to reduce the size of data.
    
     
    
 
@@ -89,7 +89,7 @@ 
    Format
    
     
    
     
    Source
    
     
    The code to prepare the .Rda file is:
    
-
    picard <- read.table("path/to/picard/duplication/output", 
+
    picard <- read.table("path/to/picard/duplication/output",
 header = TRUE, fill = TRUE) 
    CnR_H3K27ac_picard <- picard[1,] 
    usethis::use_data(CnR_H3K27ac_picard, overwrite = TRUE) 
    
     
    
 
@@ -101,19 +101,19 @@ 
    Source
    
 
 
       
    
-  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.
    
+  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/CnT_H3K27ac.html b/reference/CnT_H3K27ac.html
index f2781cb..76686ff 100644
--- a/reference/CnT_H3K27ac.html
+++ b/reference/CnT_H3K27ac.html
@@ -9,7 +9,7 @@
 
 
 
-    
+
 
     
    
       
    
 
@@ -37,7 +37,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Example CUT&Tag peak file
    
-    Source: R/data.R
+    Source: R/data.R
     
     
    
 
@@ -91,9 +91,9 @@ 
    Format
    
     
    
     
    Source
    
     
    The code to prepare the .Rda file from the raw peak file is:
    
-
    # sequences were directly downloaded from 
-https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8383507 
    # and peaks (BED file) were generated by Leyla Abbasova 
-(Neurogenomics Lab, Imperial College London) 
    CnT_H3K27ac <- ChIPseeker::readPeakFile("path", as = "GRanges") 
    CnT_H3K27ac <- CnT_H3K27ac[seqnames(CnT_H3K27ac)== "chr1"] 
    my_label <- 
+
    # sequences were directly downloaded from
+https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8383507 
    # and peaks (BED file) were generated by Leyla Abbasova
+(Neurogenomics Lab, Imperial College London) 
    CnT_H3K27ac <- ChIPseeker::readPeakFile("path", as = "GRanges") 
    CnT_H3K27ac <- CnT_H3K27ac[seqnames(CnT_H3K27ac)== "chr1"] 
    my_label <-
 c("name","score","strand","signalValue","pValue","qValue","peak") 
    colnames(GenomicRanges::mcols(CnT_H3K27ac)) <- my_label 
    usethis::use_data(CnT_H3K27ac) 
    
     
    
 
@@ -105,19 +105,19 @@ 
    Source
    
 
 
       
    
-  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.
    
+  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/CnT_H3K27ac_picard.html b/reference/CnT_H3K27ac_picard.html
index b015e64..50b1aa8 100644
--- a/reference/CnT_H3K27ac_picard.html
+++ b/reference/CnT_H3K27ac_picard.html
@@ -1,14 +1,14 @@
 
-Example Picard duplication metrics file 1 — CnT_H3K27ac_picard • EpiCompareExample Picard duplication metrics file 1 — CnT_H3K27ac_picard • EpiCompare
-    
+
 
     
    
       
    
 
@@ -36,7 +36,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Example Picard duplication metrics file 1
    
-    Source: R/data.R
+    Source: R/data.R
     
     
    
 
     
    
-    
    Duplication metrics output of CUT&Tag H3K27ac file 
+    
    Duplication metrics output of CUT&Tag H3K27ac file
 (sample accession: SRR8581604).
-Raw sequences were aligned to hg19 genome and Picard 
+Raw sequences were aligned to hg19 genome and Picard
 was performed by Leyla Abbasova.
-The duplication summary output generated by Picard was processed 
+The duplication summary output generated by Picard was processed
 to reduce the size of data.
    
     
    
 
@@ -89,7 +89,7 @@ 
    Format
    
     
    
     
    Source
    
     
    The code to prepare the .Rda file is:
    
-
    picard <- read.table("path/to/picard/duplication/output", 
+
    picard <- read.table("path/to/picard/duplication/output",
 header = TRUE, fill = TRUE)] 
    CnT_H3K27ac_picard <- picard[1,] 
    usethis::use_data(CnT_H3K27ac_picard, overwrite = TRUE) 
    
     
    
 
@@ -101,19 +101,19 @@ 
    Source
    
 
 
       
    
-  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.
    
+  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/EpiCompare.html b/reference/EpiCompare.html
index 7ea4a9f..a49e463 100644
--- a/reference/EpiCompare.html
+++ b/reference/EpiCompare.html
@@ -6,7 +6,7 @@
 
 
 
-    
+
 
     
    
       
    
 
@@ -34,7 +34,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Compare epigenomic datasets
    
-    Source: R/EpiCompare.R
+    Source: R/EpiCompare.R
     
     
    
 
@@ -111,7 +111,9 @@ 
    Compare epigenomic datasets
    
 
     
    
     
    Arguments
    
-    
    peakfiles
    
+
+
+
    peakfiles
    
 
    A list of peak files as GRanges object and/or as paths to
 BED files. If paths are provided, EpiCompare imports the file as GRanges
 object. EpiCompare also accepts a list containing a mix of GRanges objects
@@ -120,7 +122,7 @@ 
    Arguments
    
 default file names will be assigned.
    
 
 
-
    genome_build
    
+
    genome_build
    
 
    A named list indicating the human genome build used to
 generate each of the following inputs:
    • "peakfiles" : Genome build for the peakfiles input.
 Assumes genome build is the same for each element in the peakfiles
@@ -135,13 +137,13 @@ 
      Arguments
      
 genome build. For example:
      genome_build = "hg19"
    
 
 
-
    genome_build_output
    
+
    genome_build_output
    
 
    Genome build to standardise all inputs to.
 Liftovers will be performed automatically as needed.
 Default: "hg19".
    
 
 
-
    blacklist
    
+
    blacklist
    
 
    A GRanges object
  containing blacklisted genomic regions.
 Blacklists included in EpiCompare are:
    • NULL (default): Automatically selects the appropriate
@@ -153,14 +155,14 @@ 
      Arguments
      
 
    • "mm10_blacklist": Regions of mm10 genome that have anomalous
 and/or unstructured signals. mm10_blacklist
      • 
 
    • "mm9_blacklist": Blacklisted regions of mm10 genome that have been
- lifted over from mm10_blacklist. 
+ lifted over from mm10_blacklist.
  mm9_blacklist
      • 
-
    • <user_input>: A custom user-provided blacklist in 
+
    • <user_input>: A custom user-provided blacklist in
 GRanges format.
      • 
 
    
 
 
-
    picard_files
    
+
    picard_files
    
 
    A list of summary metrics output from Picard.
 Files must be in data.frame format and listed using list()
 and named using names().
@@ -169,7 +171,7 @@ 
    Arguments
    
  header = TRUE, fill = TRUE)    .
    
 
 
-
    reference
    
+
    reference
    
 
    A named list containing reference peak file(s) as GRanges
  object. Please ensure that the reference file is listed and named
 i.e. list("reference_name" = reference_peak). If more than one
@@ -180,25 +182,25 @@ 
    Arguments
    
 (2) ChromHMM of overlapping/non-overlapping peaks.
    
 
 
-
    upset_plot
    
+
    upset_plot
    
 
    Default FALSE. If TRUE, the report includes upset plot of
 overlapping peaks.
    
 
 
-
    stat_plot
    
+
    stat_plot
    
 
    Default FALSE. If TRUE, the function creates a plot showing
 the statistical significance of overlapping/non-overlapping peaks.
 Reference peak file must be provided.
    
 
 
-
    chromHMM_plot
    
+
    chromHMM_plot
    
 
    Default FALSE. If TRUE, the function outputs ChromHMM
 heatmap of individual peak files. If a reference peak file is provided,
-ChromHMM annotation of overlapping and non-overlapping peaks 
+ChromHMM annotation of overlapping and non-overlapping peaks
 is also provided.
    
 
 
-
    chromHMM_annotation
    
+
    chromHMM_annotation
    
 
    ChromHMM annotation for ChromHMM plots.
 Default K562 cell-line. Cell-line options are:
    • "K562" = K-562 cells
      • 
 
    • "Gm12878" = Cellosaurus cell-line GM12878
      • 
@@ -212,79 +214,79 @@ 
      Arguments
      
 
    
 
 
-
    chipseeker_plot
    
+
    chipseeker_plot
    
 
    Default FALSE. If TRUE, the report includes a barplot
 of ChIPseeker annotation of peak files.
    
 
 
-
    enrichment_plot
    
+
    enrichment_plot
    
 
    Default FALSE. If TRUE, the report includes dotplots
 of KEGG and GO enrichment analysis of peak files.
    
 
 
-
    tss_plot
    
+
    tss_plot
    
 
    Default FALSE. If TRUE, the report includes peak count
 frequency around transcriptional start site. Note that this can take awhile.
    
 
 
-
    tss_distance
    
+
    tss_distance
    
 
    A vector specifying the distance upstream and downstream
-around transcription start sites (TSS). 
-The default value is c(-3000,3000); meaning peak frequency 
+around transcription start sites (TSS).
+The default value is c(-3000,3000); meaning peak frequency
 3000bp upstream and downstream of TSS will be displayed.
    
 
 
-
    precision_recall_plot
    
+
    precision_recall_plot
    
 
    Default is FALSE. If TRUE,
 creates a precision-recall curve plot and an F1 plot using
 plot_precision_recall.
    
 
 
-
    n_threshold
    
+
    n_threshold
    
 
    Number of thresholds to test.
    
 
 
-
    corr_plot
    
+
    corr_plot
    
 
    Default is FALSE. If TRUE, creates a correlation plot across
 all peak files using
 plot_corr.
    
 
 
-
    bin_size
    
+
    bin_size
    
 
    Default of 100. Base-pair size of the bins created to measure
-correlation. Use smaller value for higher resolution but longer run time and 
+correlation. Use smaller value for higher resolution but longer run time and
 larger memory usage.
    
 
 
-
    interact
    
+
    interact
    
 
    Default TRUE. By default, plots are interactive.
 If set FALSE, all plots in the report will be static.
    
 
 
-
    add_download_button
    
+
    add_download_button
    
 
    Add download buttons for each plot or dataset.
    
 
 
-
    save_output
    
+
    save_output
    
 
    Default FALSE. If TRUE, all outputs (tables and plots) of
 the analysis will be saved in a folder (EpiCompare_file).
    
 
 
-
    output_filename
    
+
    output_filename
    
 
    Default EpiCompare.html. If otherwise, the html report
 will be saved in the specified name.
    
 
 
-
    output_timestamp
    
+
    output_timestamp
    
 
    Default FALSE. If TRUE, date will be included in the
 file name.
    
 
 
-
    output_dir
    
+
    output_dir
    
 
    Path to where output HTML file should be saved.
    
 
 
-
    display
    
+
    display
    
 
    After completion, automatically display the HTML report file
  in one of the following ways:
    • "browser" : Display the report in your default web browser.
      • 
 
    • "rsstudio" : Display the report in Rstudio.
      • 
@@ -292,40 +294,38 @@ 
      Arguments
      
 
    
 
 
-
    run_all
    
+
    run_all
    
 
    Convenience argument that enables all plots/features
 (without specifying each argument manually)
  by overriding the default values.
  Default: FALSE.
    
 
 
-
    workers
    
+
    workers
    
 
    Number of threads to parallelize across.
    
 
 
-
    quiet
    
+
    quiet
    
 
    An option to suppress printing during rendering from knitr,
 pandoc command line and others. To only suppress printing of the last
 "Output created: " message, you can set rmarkdown.render.message to
 FALSE
    
 
 
-
    error
    
-
    If TRUE, the Rmarkdown report will continue to render 
+
    error
    
+
    If TRUE, the Rmarkdown report will continue to render
 even when some chunks encounter errors (default: FALSE).
 Passed to opts_chunk.
    
 
 
-
    debug
    
-
    Run in debug mode, where are messages and warnings 
+
    debug
    
+
    Run in debug mode, where are messages and warnings
 are printed within the HTML report (default: FALSE).
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Path to one or more HTML report files.
    
+    
    Path to one or more HTML report files.
    
     
    
 
     
    
@@ -426,11 +426,11 @@ 
    Examples
    
 #> 58/59 [Session Info]            
 #> 59/59                           
 #> output file: EpiCompare.knit.md
-#> /usr/local/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp2pySPs/EpiCompare_test.html --lua-filter /__w/_temp/Library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /__w/_temp/Library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /__w/_temp/Library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css custom.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp2pySPs/rmarkdown-str82a44b357c37.html --variable code_folding=hide --variable code_menu=1 
+#> /usr/bin/pandoc +RTS -K512m -RTS EpiCompare.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpKu2U4A/EpiCompare_test.html --lua-filter /__w/_temp/Library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /__w/_temp/Library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /__w/_temp/Library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /__w/_temp/Library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css custom.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpKu2U4A/rmarkdown-str44305c4cc624.html --variable code_folding=hide --variable code_menu=1 
 #> 
-#> Output created: /tmp/Rtmp2pySPs/EpiCompare_test.html
-#> [1] "Done in 0.1 min."
-#> All outputs saved to: /tmp/Rtmp2pySPs
+#> Output created: /tmp/RtmpKu2U4A/EpiCompare_test.html
+#> [1] "Done in 0.09 min."
+#> All outputs saved to: /tmp/RtmpKu2U4A
 # utils::browseURL(output_html)
    @@ -442,19 +442,19 @@

    Examples

    - - + + diff --git a/reference/as_interactive.html b/reference/as_interactive.html index 6951c56..9c9fd55 100644 --- a/reference/as_interactive.html +++ b/reference/as_interactive.html @@ -1,10 +1,10 @@ -As interactive — as_interactive • EpiCompareAs interactive — as_interactive • EpiCompare - +
    @@ -32,7 +32,7 @@
    • - +

    As interactive

    - Source: R/as_interactive.R + Source: R/as_interactive.R
    -

    Convert a ggplot object to plotly, +

    Convert a ggplot object to plotly, and enable it to be plotted within an Rmarkdown HTML file.

    @@ -85,28 +85,26 @@

    Source

    Arguments

    -
    plt
    + + +
    plt

    ggplot object.

    -
    to_widget
    +
    to_widget

    Convert to a widget so it works within Rmarkdown HTML files. -By default, this will be only be set to TRUE when being run within +By default, this will be only be set to TRUE when being run within the context of knitr rendering.

    -
    add_boxmode
    +
    add_boxmode

    Add extra layout to enable dodged boxplots.

    Value

    - - -

    A plotly object or a tagList

    - - -

    wrapping the plotly object.

    +

    A plotly object or a tagList +wrapping the plotly object.

    @@ -117,19 +115,19 @@

    Value

    - - + + diff --git a/reference/bpplapply.html b/reference/bpplapply.html index 0e9c1e4..3ee8bed 100644 --- a/reference/bpplapply.html +++ b/reference/bpplapply.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Wrapper for bplapply

    - Source: R/bpplapply.R + Source: R/bpplapply.R
    @@ -86,45 +86,47 @@

    Wrapper for

    Arguments

    -
    X
    + + +
    X

    Any object for which methods length, [, and [[ are implemented.

    -
    FUN
    +
    FUN

    The function to be applied to each element of X.

    -
    apply_fun
    +
    apply_fun

    Iterator function to use.

    -
    workers
    +
    workers

    Number of threads to parallelize across.

    -
    progressbar
    +
    progressbar

    logical(1) Enable progress bar (based on plyr:::progress_text).

    -
    verbose
    +
    verbose

    Print messages.

    -
    use_snowparam
    +
    use_snowparam

    Whether to use SnowParam (default: TRUE) or MulticoreParam (FALSE) when parallelising across multiple workers.

    -
    register_now
    +
    register_now

    Register the cores now with register (TRUE), or simply return the BPPARAM object (default: FALSE).

    -
    ...
    +
    ...

    Arguments passed on to BiocParallel::bplapply

    BPPARAM

    An optional BiocParallelParam instance determining the parallel back-end to be used during evaluation, or a @@ -140,15 +142,13 @@

    Arguments

    BPOPTIONS

    Additional options to control the behavior of the parallel evaluation, see bpoptions.

    - +

    Value

    - - -

    (Named) list.

    +

    (Named) list.

    @@ -165,19 +165,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/checkCache.html b/reference/checkCache.html index 8e400e1..9f9cfc5 100644 --- a/reference/checkCache.html +++ b/reference/checkCache.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Check cache

    - Source: R/checkCache.R + Source: R/checkCache.R
    @@ -74,19 +74,19 @@

    Check cache

    Arguments

    -
    cache
    + + +
    cache

    BiocFileCache.

    -
    url
    +
    url

    Path to cached file.

    Value

    - - -

    path

    +

    path

    @@ -97,19 +97,19 @@

    Value

    - - + + diff --git a/reference/check_cell_lines.html b/reference/check_cell_lines.html index 223a72c..5c9a606 100644 --- a/reference/check_cell_lines.html +++ b/reference/check_cell_lines.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Check cell lines

    - Source: R/check_cell_lines.R + Source: R/check_cell_lines.R
    @@ -76,20 +76,20 @@

    Check cell lines

    Arguments

    -
    cell_lines
    + + +
    cell_lines

    A character vector of cell line names. If NULL (default), will return names of all cell lines.

    -
    verbose
    +
    verbose

    Print messages.

    Value

    - - -

    Character vector, or NULL.

    +

    Character vector, or NULL.

    @@ -100,19 +100,19 @@

    Value

    - - + + diff --git a/reference/check_genome_build.html b/reference/check_genome_build.html index 06a89f5..376af58 100644 --- a/reference/check_genome_build.html +++ b/reference/check_genome_build.html @@ -1,10 +1,10 @@ -Check genome build — check_genome_build • EpiCompareCheck genome build — check_genome_build • EpiCompare - +
    @@ -32,7 +32,7 @@
    • - +

    Check genome build

    - Source: R/check_genome_build.R + Source: R/check_genome_build.R
    -

    Check that the genome build is valid and +

    Check that the genome build is valid and require specific reference datasets to be installed.

    @@ -76,19 +76,19 @@

    Check genome build

    Arguments

    -
    genome_build
    + + +
    genome_build

    Genome build name.

    -
    type
    +
    type

    whether to fetch the txdb or bsgen reference data

    Value

    - - -

    txdb or bsgen

    +

    txdb or bsgen

    @@ -99,19 +99,19 @@

    Value

    - - + + diff --git a/reference/check_grlist_cols.html b/reference/check_grlist_cols.html index bc87dd0..c84499f 100644 --- a/reference/check_grlist_cols.html +++ b/reference/check_grlist_cols.html @@ -1,11 +1,11 @@ -Check GRanges list columns — check_grlist_cols • EpiCompareCheck GRanges list columns — check_grlist_cols • EpiCompare - +
    @@ -33,7 +33,7 @@
    • - +

    Check GRanges list columns

    - Source: R/check_grlist_cols.R + Source: R/check_grlist_cols.R
    -

    Check that at least one of the required columns is in +

    Check that at least one of the required columns is in a list of GRanges objects. Elements that do not meet this criterion will be dropped from the list.

    @@ -78,19 +78,19 @@

    Check

    Arguments

    -
    grlist
    + + +
    grlist

    Named list of GRanges objects.

    -
    target_cols
    +
    target_cols

    A character vector of column names to search for.

    Value

    - - -

    Named list of GRanges objects.

    +

    Named list of GRanges objects.

    @@ -101,19 +101,19 @@

    Value

    - - + + diff --git a/reference/check_list_names.html b/reference/check_list_names.html index 1169407..238cfcd 100644 --- a/reference/check_list_names.html +++ b/reference/check_list_names.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Check peaklist is named

    - Source: R/check_list_names.R + Source: R/check_list_names.R
    @@ -76,20 +76,20 @@

    Check peaklist is named

    Arguments

    -
    peaklist
    + + +
    peaklist

    A list of peak files as GRanges object.

    -
    default_prefix
    +
    default_prefix

    Default prefix to use when creating names for peaklist.

    Value

    - - -

    named peaklist

    +

    named peaklist

    @@ -100,19 +100,19 @@

    Value

    - - + + diff --git a/reference/check_workers.html b/reference/check_workers.html index 074318d..bf0327f 100644 --- a/reference/check_workers.html +++ b/reference/check_workers.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Check workers

    - Source: R/check_workers.R + Source: R/check_workers.R
    @@ -74,17 +74,17 @@

    Check workers

    Arguments

    -
    workers
    -

    Number of cores to parallelise across + + +

    workers
    +

    Number of cores to parallelise across (in applicable functions). If NULL, will set to the total number of available cores minus 1.

    Value

    - - -

    Integer

    +

    Integer

    @@ -100,19 +100,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/clean_granges.html b/reference/clean_granges.html index 66f6e34..cc33496 100644 --- a/reference/clean_granges.html +++ b/reference/clean_granges.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Clean GRanges

    - Source: R/clean_granges.R + Source: R/clean_granges.R
    @@ -80,19 +80,19 @@

    Clean GRanges

    Arguments

    -
    gr
    + + +
    gr

    A GRanges object.

    -
    nono_cols
    +
    nono_cols

    Problematic columns to search for and remove (if present).

    Value

    - - -

    Cleaned GRanges object.

    +

    Cleaned GRanges object.

    @@ -103,19 +103,19 @@

    Value

    - - + + diff --git a/reference/compute_consensus_peaks.html b/reference/compute_consensus_peaks.html index 9067ea0..aced72e 100644 --- a/reference/compute_consensus_peaks.html +++ b/reference/compute_consensus_peaks.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Compute consensus peaks

    - Source: R/compute_consensus_peaks.R + Source: R/compute_consensus_peaks.R
    @@ -90,41 +90,43 @@

    Source

    Arguments

    -
    grlist
    + + +
    grlist

    Named list of GRanges objects.

    -
    groups
    -

    A character vector of the same length as grlist -defining how to group GRanges objects when +

    groups
    +

    A character vector of the same length as grlist +defining how to group GRanges objects when computing consensus peaks.

    -
    genome_build
    +
    genome_build

    Genome build name.

    -
    lower, upper
    +
    lower, upper

    The lower and upper bounds for the slice.

    -
    min.gapwidth
    +
    min.gapwidth

    Ranges separated by a gap of at least min.gapwidth positions are not merged.

    -
    method
    -

    Method to call peaks with:

    • "granges" : Simple overlap procedure using +

      method
      +

      Method to call peaks with:

      • "granges" : Simple overlap procedure using GRanges functions. Faster but less accurate.

        • -

      • "consensusseeker" : +

      • "consensusseeker" : Uses findConsensusPeakRegions to compute consensus -peaks. +peaks. Slower but more accurate.

      -
      ...
      +
      ...

      Arguments passed on to consensusSeekeR::findConsensusPeakRegions

      narrowPeaks

      a GRanges containing called peak regions of signal enrichment based on pooled, normalized data @@ -185,23 +187,21 @@

      Arguments

      number of threads to use in parallel. The nbrThreads must be a positive integer. Default = 1.

      - +

    Value

    - - -

    Named list of consensus peak GRanges.

    +

    Named list of consensus peak GRanges.

    Details

    -

    NOTE: If you get the error +

    NOTE: If you get the error "Error in serialize(data, node$con) : error writing to connection", -try running closeAllConnections -and rerun compute_consensus_peaks. -This error can sometimes occur when +try running closeAllConnections +and rerun compute_consensus_peaks. +This error can sometimes occur when compute_consensus_peaks has been disrupted partway through.

    @@ -237,19 +237,19 @@

    Examples

    - - + + diff --git a/reference/compute_corr.html b/reference/compute_corr.html index 62fbe0e..99c887b 100644 --- a/reference/compute_corr.html +++ b/reference/compute_corr.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Compute correlation matrix

    - Source: R/compute_corr.R + Source: R/compute_corr.R
    @@ -87,7 +87,9 @@

    Compute correlation matrix

    Arguments

    -
    peakfiles
    + + +
    peakfiles

    A list of peak files as GRanges object and/or as paths to BED files. If paths are provided, EpiCompare imports the file as GRanges object. EpiCompare also accepts a list containing a mix of GRanges objects @@ -96,7 +98,7 @@

    Arguments

    default file names will be assigned.

    -
    reference
    +
    reference

    A named list containing reference peak file(s) as GRanges object. Please ensure that the reference file is listed and named i.e. list("reference_name" = reference_peak). If more than one @@ -107,76 +109,74 @@

    Arguments

    (2) ChromHMM of overlapping/non-overlapping peaks.

    -
    genome_build
    -

    The build of **all** peak and reference files to -calculate the correlation matrix on. If all peak and reference files are not -of the same build use +

    genome_build
    +

    The build of **all** peak and reference files to +calculate the correlation matrix on. If all peak and reference files are not +of the same build use liftover_grlist to convert them all before running. Genome build should be one of hg19, hg38, mm9, mm10.

    -
    keep_chr
    +
    keep_chr

    Which chromosomes to keep.

    -
    drop_empty_chr
    -

    Drop chromosomes that are not present in any of the +

    drop_empty_chr
    +

    Drop chromosomes that are not present in any of the peakfiles (default: FALSE).

    -
    bin_size
    +
    bin_size

    Default of 100. Base-pair size of the bins created to measure -correlation. Use smaller value for higher resolution but longer run time and +correlation. Use smaller value for higher resolution but longer run time and larger memory usage.

    -
    method
    -

    Default spearman (i.e. non-parametric). A character string -indicating which correlation coefficient (or covariance) is to be computed. +

    method
    +

    Default spearman (i.e. non-parametric). A character string +indicating which correlation coefficient (or covariance) is to be computed. One of "pearson", "kendall", or "spearman": can be abbreviated.

    -
    intensity_cols
    +
    intensity_cols

    Depending on which columns are present, this -value will be used to get quantiles and ultimately calculate the -correlations:

    • "total_signal" : Used by the peak calling software - SEACR. - NOTE: Another SEACR column (e.g. "max_signal") can be used +value will be used to get quantiles and ultimately calculate the +correlations:

      • "total_signal" : Used by the peak calling software + SEACR. + NOTE: Another SEACR column (e.g. "max_signal") can be used together or instead of "total_signal".

        • -

      • "qValue"Used by the peak calling software - MACS2/3. - Should contain the negative log of the p-values after multiple +

      • "qValue"Used by the peak calling software + MACS2/3. + Should contain the negative log of the p-values after multiple testing correction.

        • -

      • "Peak Score" : +

      • "Peak Score" : Used by the peak calling software HOMER.

    -
    return_bins
    +
    return_bins

    If TRUE, returns a named list - with both the rebinned + with both the rebinned (standardised) peaks ("bin") and the correlation matrix ("cor"). If FALSE (default), returns only the correlation matrix (unlisted).

    -
    fill_diag
    +
    fill_diag

    Fill the diagonal of the overlap matrix.

    -
    workers
    +
    workers

    Number of threads to parallelize across.

    -
    save_path
    +
    save_path

    Path to save a table of correlation results to.

    Value

    - - -

    correlation matrix

    +

    correlation matrix

    @@ -199,7 +199,7 @@

    Examples

    #> Matrix sparsity: 0.9646 #> Calculating correlation matrix. #> Done computing correlations in 1 seconds. -#> Saving correlation results ==> /tmp/Rtmp2pySPs/file82a461680aea.corr.csv.gz +#> Saving correlation results ==> /tmp/RtmpKu2U4A/file44302aee9381.corr.csv.gz
    @@ -210,19 +210,19 @@

    Examples

    - - + + diff --git a/reference/download_button.html b/reference/download_button.html index 9fd55f8..56755c1 100644 --- a/reference/download_button.html +++ b/reference/download_button.html @@ -5,7 +5,7 @@ - +
    @@ -33,7 +33,7 @@
    • - +

    Download local file

    - Source: R/download_button.R + Source: R/download_button.R
    @@ -97,59 +97,59 @@

    Source

    Arguments

    -
    object
    + + +
    object

    R object to serialize.

    -
    save_output
    +
    save_output

    Default FALSE. If TRUE, all outputs (tables and plots) of the analysis will be saved in a folder (EpiCompare_file).

    -
    outfile_dir
    +
    outfile_dir

    Directory to save the file to.

    -
    filename
    +
    filename

    Name of the file to save.

    -
    button_label
    +
    button_label

    Character (HTML), button label

    -
    output_extension
    +
    output_extension

    Extension of the output file. Currently, .csv, .xlsx, and .rds are supported. If a (named) list is passed to the function, only .xlsx and .rds are supported.

    -
    icon
    +
    icon

    Fontawesome tag e.g.: "fa fa-save"

    -
    button_type
    +
    button_type

    Character, one of the standard Bootstrap types

    -
    self_contained
    +
    self_contained

    A boolean to specify whether your HTML output is self-contained. Default to FALSE.

    -
    add_download_button
    +
    add_download_button

    Add download buttons for each plot or dataset.

    -
    verbose
    +
    verbose

    Print messages.

    Value

    - - -

    Download button as HTML text.

    +

    Download button as HTML text.

    @@ -165,19 +165,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/encode_H3K27ac.html b/reference/encode_H3K27ac.html index 27a360a..b08cb18 100644 --- a/reference/encode_H3K27ac.html +++ b/reference/encode_H3K27ac.html @@ -8,7 +8,7 @@ - +
    @@ -36,7 +36,7 @@
    • - +

    Example ChIP-seq peak file

    - Source: R/data.R + Source: R/data.R
    @@ -90,7 +90,7 @@

    Format

    Source

    The code to prepare the .Rda file from the raw peak file is:

    # dataset was directly downloaded from
    # https://www.encodeproject.org/files/ENCFF044JNJ/ -encode_H3K27ac <- ChIPseeker::readPeakFile("path", as = "GRanges")
    encode_H3K27ac <- +encode_H3K27ac <- ChIPseeker::readPeakFile("path", as = "GRanges")
    encode_H3K27ac <- encode_H3K27ac[seqnames(encode_H3K27ac) == "chr1"]
    my_label <- c("name","score","strand","signalValue","pValue","qValue","peak")
    colnames(GenomicRanges::mcols(encode_H3K27ac)) <- my_label
    usethis::use_data(encode_H3K27ac, overwrite = TRUE)

    @@ -103,19 +103,19 @@

    Source

    - - + + diff --git a/reference/fig_length.html b/reference/fig_length.html index 1d882ff..171bf36 100644 --- a/reference/fig_length.html +++ b/reference/fig_length.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Dynamic Figure Length Generator

    - Source: R/fig_length.R + Source: R/fig_length.R
    @@ -76,23 +76,23 @@

    Dynamic Figure Length Generator

    Arguments

    -
    default_size
    + + +
    default_size

    The default figure length. Must be numeric.

    -
    number_of_items
    +
    number_of_items

    Number of peak files, or terms.

    -
    max_items
    +
    max_items

    Maximum number of peak files, or terms.

    Value

    - - -

    Figure height/width. A number.

    +

    Figure height/width. A number.

    @@ -103,19 +103,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/fragment_info.html b/reference/fragment_info.html index bdd968f..c90000d 100644 --- a/reference/fragment_info.html +++ b/reference/fragment_info.html @@ -5,7 +5,7 @@ - +
    @@ -33,7 +33,7 @@
    • - +

    Summary on fragments

    - Source: R/fragment_info.R + Source: R/fragment_info.R
    @@ -78,7 +78,9 @@

    Summary on fragments

    Arguments

    -
    picard_list
    + + +
    picard_list

    Named list of duplication metrics generated by Picard as data frame. Data frames must be named and listed using list(). e.g. list("name1"=file1, "name2"=file2). @@ -89,9 +91,7 @@

    Arguments

    Value

    - - -

    A table summarizing metrics on fragments.

    +

    A table summarizing metrics on fragments.

    @@ -119,19 +119,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/gather_files.html b/reference/gather_files.html index 8399bb4..3f8113f 100644 --- a/reference/gather_files.html +++ b/reference/gather_files.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Gather files

    - Source: R/gather_files.R + Source: R/gather_files.R
    @@ -84,11 +84,13 @@

    Gather files

    Arguments

    -
    dir
    + + +
    dir

    Directory to search within.

    -
    type
    +
    type

    File type to search for. Options include:

    • "<pattern>"Finds files matching an arbitrary regex pattern specified by user.

    • "peaks.stringent"Finds files ending in "*.stringent.bed$"

      • @@ -100,47 +102,45 @@

      Arguments

    -
    nfcore_cutandrun
    +
    nfcore_cutandrun

    Whether the files were generated by the nf-core/cutandrun Nextflow pipeline. If TRUE, can use the standardised folder structure to automatically generate more descriptive file names with sample IDs.

    -
    return_paths
    -

    Return only the file paths without actually reading them +

    return_paths
    +

    Return only the file paths without actually reading them in as GRanges.

    -
    rbind_list
    +
    rbind_list

    Bind all objects into one.

    -
    workers
    -

    Number of cores to parallelise across +

    workers
    +

    Number of cores to parallelise across (in applicable functions). If NULL, will set to the total number of available cores minus 1.

    -
    verbose
    +
    verbose

    Print messages.

    Value

    - - -

    A named list of GRanges objects.

    +

    A named list of GRanges objects.

    Details

    -

    For "peaks.stringent" files called with +

    For "peaks.stringent" files called with SEACR, column names will be automatically added:

    • total_signal : Total signal contained within denoted coordinates.

      • -

    • max_signalMaximum bedgraph signal attained at any base pair +

    • max_signalMaximum bedgraph signal attained at any base pair within denoted coordinates.

      • -

    • max_signal_region Region representing the farthest upstream -and farthest downstream bases within the denoted coordinates +

    • max_signal_region Region representing the farthest upstream +and farthest downstream bases within the denoted coordinates that are represented by the maximum bedgraph signal.

    @@ -148,9 +148,9 @@

    Details

    Examples

    #### Make example files ####
 save_paths <- EpiCompare::write_example_peaks()
-#> Writing ==> /tmp/Rtmp2pySPs/processed_results/encode_H3K27ac.narrowPeaks.bed
-#> Writing ==> /tmp/Rtmp2pySPs/processed_results/CnT_H3K27ac.narrowPeaks.bed
-#> Writing ==> /tmp/Rtmp2pySPs/processed_results/CnR_H3K27ac.narrowPeaks.bed
+#> Writing ==> /tmp/RtmpKu2U4A/processed_results/encode_H3K27ac.narrowPeaks.bed
+#> Writing ==> /tmp/RtmpKu2U4A/processed_results/CnT_H3K27ac.narrowPeaks.bed
+#> Writing ==> /tmp/RtmpKu2U4A/processed_results/CnR_H3K27ac.narrowPeaks.bed
 dir <- unique(dirname(save_paths))
 #### Gather/import files ####
 peaks <- EpiCompare::gather_files(dir=dir, 
@@ -171,19 +171,19 @@ 
    Examples
    
 
 
       
    
-  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.
    
+  
    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    - - + + diff --git a/reference/gather_files_names.html b/reference/gather_files_names.html index 7615335..013414e 100644 --- a/reference/gather_files_names.html +++ b/reference/gather_files_names.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Make file names

    - Source: R/gather_files_names.R + Source: R/gather_files_names.R
    @@ -74,11 +74,13 @@

    Make file names

    Arguments

    -
    paths
    + + +
    paths

    Character vector of file paths.

    -
    type
    +
    type

    File type to search for. Options include:

    • "<pattern>"Finds files matching an arbitrary regex pattern specified by user.

    • "peaks.stringent"Finds files ending in "*.stringent.bed$"

      • @@ -90,22 +92,20 @@

      Arguments

    -
    nfcore_cutandrun
    +
    nfcore_cutandrun

    Whether the files were generated by the nf-core/cutandrun Nextflow pipeline. If TRUE, can use the standardised folder structure to automatically generate more descriptive file names with sample IDs.

    -
    verbose
    +
    verbose

    Print messages.

    Value

    - - -

    Named character vector.

    +

    Named character vector.

    @@ -116,19 +116,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/get_bpparam.html b/reference/get_bpparam.html index 61e5089..fac7bca 100644 --- a/reference/get_bpparam.html +++ b/reference/get_bpparam.html @@ -1,13 +1,13 @@ -Get BiocParallel parameters — get_bpparam • EpiCompareGet BiocParallel parameters — get_bpparam • EpiCompare - +
    @@ -35,7 +35,7 @@
    • - +

    Get BiocParallel parameters

    - Source: R/get_bpparam.R + Source: R/get_bpparam.R
    -

    Get (and optionally register) BiocParallel parameter +

    Get (and optionally register) BiocParallel parameter (BPPARAM). SnowParam is the default function -as it tends to be more robust. However, because it doesn't work on Windows, -this function automatically detected the Operating System and switches +as it tends to be more robust. However, because it doesn't work on Windows, +this function automatically detected the Operating System and switches to SerialParam as needed.

    @@ -87,22 +87,24 @@

    Get

    Arguments

    -
    workers
    + + +
    workers

    Number of threads to parallelize across.

    -
    progressbar
    +
    progressbar

    logical(1) Enable progress bar (based on plyr:::progress_text).

    -
    use_snowparam
    +
    use_snowparam

    Whether to use SnowParam (default: TRUE) or MulticoreParam (FALSE) when parallelising across multiple workers.

    -
    register_now
    +
    register_now

    Register the cores now with register (TRUE), or simply return the BPPARAM object (default: FALSE).

    @@ -110,9 +112,7 @@

    Arguments

    Value

    - - -

    BPPARAM

    +

    BPPARAM

    @@ -123,19 +123,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/get_chromHMM_annotation.html b/reference/get_chromHMM_annotation.html index ac9c664..b95b8a2 100644 --- a/reference/get_chromHMM_annotation.html +++ b/reference/get_chromHMM_annotation.html @@ -1,16 +1,16 @@ Download ChromHMM annotation file(s) — get_chromHMM_annotation • EpiCompare - +
    @@ -38,7 +38,7 @@
    • - +

    Download ChromHMM annotation file(s)

    - Source: R/get_chromHMM_annotation.R + Source: R/get_chromHMM_annotation.R

    Download ChromHMM annotation file(s) for a given cell-line - (returned as a GRanges object) + (returned as a GRanges object) or a list of cell-lines (returned as a named list of GRanges objects). All annotations are aligned to the hg19 genome build. - All data can be found on the UCSC Genome Browser + All data can be found on the UCSC Genome Browser here.

    @@ -91,7 +91,9 @@

    Download ChromHMM annotation file(s)

    Arguments

    -
    cell_line
    + + +
    cell_line

    ChromHMM annotation for user-specified cell-line. Cell-line options are:

    • "K562" = K-562 cells

    • "Gm12878" = Cellosaurus cell-line GM12878

      • @@ -107,9 +109,7 @@

      Arguments

    Value

    - - -

    Cell-line specific ChromHMM annotation file. Default K562 cell-line.

    +

    Cell-line specific ChromHMM annotation file. Default K562 cell-line.

    @@ -120,19 +120,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/group_files.html b/reference/group_files.html index 3158412..8f6d2d2 100644 --- a/reference/group_files.html +++ b/reference/group_files.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Group files

    - Source: R/group_files.R + Source: R/group_files.R
    @@ -76,7 +76,9 @@

    Group files

    Arguments

    -
    peakfiles
    + + +
    peakfiles

    A list of peak files as GRanges object and/or as paths to BED files. If paths are provided, EpiCompare imports the file as GRanges object. EpiCompare also accepts a list containing a mix of GRanges objects @@ -85,15 +87,13 @@

    Arguments

    default file names will be assigned.

    -
    searches
    +
    searches

    A named list of substrings to group peakfiles by.

    Value

    - - -

    Named peak files

    +

    Named peak files

    @@ -118,19 +118,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/hg19_blacklist.html b/reference/hg19_blacklist.html index 46cc354..7146c02 100644 --- a/reference/hg19_blacklist.html +++ b/reference/hg19_blacklist.html @@ -6,7 +6,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +

    Human genome hg19 blacklisted regions

    - Source: R/data.R + Source: R/data.R
    @@ -85,7 +85,7 @@

    Format

    Source

    The code to prepare the .Rda file is:

    -

    # blacklisted regions were directly downloaded
    # from https://www.encodeproject.org/files/ENCFF001TDO/
    hg19_blacklist <- +

    # blacklisted regions were directly downloaded
    # from https://www.encodeproject.org/files/ENCFF001TDO/
    hg19_blacklist <- ChIPseeker::readPeakFile(file.path(path), as = "GRanges")
    usethis::use_data(hg19_blacklist, overwrite = TRUE)

    @@ -97,19 +97,19 @@

    Source

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/hg38_blacklist.html b/reference/hg38_blacklist.html index a45378c..8b46373 100644 --- a/reference/hg38_blacklist.html +++ b/reference/hg38_blacklist.html @@ -1,13 +1,13 @@ Human genome hg38 blacklisted regions — hg38_blacklist • EpiCompare - +
    @@ -35,7 +35,7 @@
    • - +

    Human genome hg38 blacklisted regions

    - Source: R/data.R + Source: R/data.R

    Obtained from https://www.encodeproject.org/files/ENCFF356LFX/. -The ENCODE blacklist includes regions of the hg38 genome that have -anomalous and/or unstructured signals +The ENCODE blacklist includes regions of the hg38 genome that have +anomalous and/or unstructured signals independent of the cell-line or experiment. Removal of ENCODE blacklist is recommended for quality measure.

    @@ -87,7 +87,7 @@

    Format

    Source

    The code to prepare the .Rda file is:

    -

    ## blacklisted regions were directly downloaded
    ## from https://www.encodeproject.org/files/ENCFF356LFX/
    hg38_blacklist <- +

    ## blacklisted regions were directly downloaded
    ## from https://www.encodeproject.org/files/ENCFF356LFX/
    hg38_blacklist <- ChIPseeker::readPeakFile(file.path(path), as = "GRanges")
    usethis::use_data(hg38_blacklist, overwrite = TRUE)

    @@ -99,19 +99,19 @@

    Source

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/index.html b/reference/index.html index 1231be3..6ebec73 100644 --- a/reference/index.html +++ b/reference/index.html @@ -1,9 +1,9 @@ -Function reference • EpiComparePackage index • EpiCompare - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -231,19 +231,19 @@

    All functions
    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/is_granges.html b/reference/is_granges.html index e463029..5847bc2 100644 --- a/reference/is_granges.html +++ b/reference/is_granges.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Is an object of class GRanges

    - Source: R/is_granges.R + Source: R/is_granges.R
    @@ -74,15 +74,15 @@

    Is an object of class GRanges

    Arguments

    -
    obj
    + + +
    obj

    Any R object.

    Value

    - - -

    Boolean.

    +

    Boolean.

    @@ -93,19 +93,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/liftover_grlist.html b/reference/liftover_grlist.html index a6b3045..d678cf9 100644 --- a/reference/liftover_grlist.html +++ b/reference/liftover_grlist.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Liftover peak list

    - Source: R/liftover_grlist.R + Source: R/liftover_grlist.R
    @@ -85,50 +85,50 @@

    Liftover peak list

    Arguments

    -
    grlist
    + + +
    grlist

    A named list of GRanges objects, or simply a single unlisted GRanges object. Can perform liftover within species or across species.

    -
    input_build
    +
    input_build

    The genome build of grlist.

    -
    output_build
    +
    output_build

    Desired genome build for grlist to be lifted over to.

    -
    style
    +
    style

    Chromosome style, set by seqlevelsStyle.

    • "UCSC" : Uses the chromosome style "chr1".

    • "NCBI" : Uses the chromosome style "1"

    -
    keep_chr
    +
    keep_chr

    Which chromosomes to keep.

    -
    as_grangeslist
    +
    as_grangeslist

    Return as a GRangesList.

    -
    merge_all
    +
    merge_all

    Merge all GRanges into a single GRanges object.

    -
    verbose
    +
    verbose

    Print messages.

    Value

    - - -

    Named list of lifted GRanges objects.

    +

    Named list of lifted GRanges objects.

    @@ -155,19 +155,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/message_parallel.html b/reference/message_parallel.html index bdff0f1..189b9e3 100644 --- a/reference/message_parallel.html +++ b/reference/message_parallel.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Message parallel

    - Source: R/message_parallel.R + Source: R/message_parallel.R
    @@ -74,9 +74,7 @@

    Message parallel

    Value

    - - -

    A message

    +

    A message

    @@ -87,19 +85,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/messager.html b/reference/messager.html index 3c78b35..4f5e636 100644 --- a/reference/messager.html +++ b/reference/messager.html @@ -1,12 +1,12 @@ Print messages — messager • EpiCompare - +
    @@ -34,7 +34,7 @@
    • - +

    Print messages

    - Source: R/messager.R + Source: R/messager.R

    Conditionally print messages. - Allows developers to easily control verbosity of functions, - and meet Bioconductor requirements that dictate the message + Allows developers to easily control verbosity of functions, + and meet Bioconductor requirements that dictate the message must first be stored to a variable before passing to message.

    @@ -80,20 +80,20 @@

    Print messages

    Arguments

    -
    v
    + + +
    v

    Whether to print messages or not.

    -
    parallel
    -

    Whether to enable message print when wrapped +

    parallel
    +

    Whether to enable message print when wrapped in parallelised functions.

    Value

    - - -

    Null

    +

    Null

    @@ -104,19 +104,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/mm10_blacklist.html b/reference/mm10_blacklist.html index 04ba2a8..fbb1f59 100644 --- a/reference/mm10_blacklist.html +++ b/reference/mm10_blacklist.html @@ -1,12 +1,12 @@ Mouse genome mm10 blacklisted regions — mm10_blacklist • EpiCompare - +
    @@ -34,7 +34,7 @@
    • - +

    Mouse genome mm10 blacklisted regions

    - Source: R/data.R + Source: R/data.R

    Obtained from https://www.encodeproject.org/files/ENCFF547MET/. -The ENCODE blacklist includes regions of the mm10 genome that have anomalous -and/or unstructured signals independent of the cell-line or experiment. +The ENCODE blacklist includes regions of the mm10 genome that have anomalous +and/or unstructured signals independent of the cell-line or experiment. Removal of ENCODE blacklist is recommended for quality measure.

    @@ -85,7 +85,7 @@

    Format

    Source

    The code to prepare the .Rda file is:

    -

    ## blacklisted regions were directly downloaded
    ## from https://www.encodeproject.org/files/ENCFF547MET/
    mm10_blacklist <- +

    ## blacklisted regions were directly downloaded
    ## from https://www.encodeproject.org/files/ENCFF547MET/
    mm10_blacklist <- ChIPseeker::readPeakFile(file.path(path), as = "GRanges")
    usethis::use_data(mm10_blacklist, overwrite = TRUE)

    @@ -97,19 +97,19 @@

    Source

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/mm9_blacklist.html b/reference/mm9_blacklist.html index a5e08fe..287616f 100644 --- a/reference/mm9_blacklist.html +++ b/reference/mm9_blacklist.html @@ -1,10 +1,10 @@ -Mouse genome mm9 blacklisted regions — mm9_blacklist • EpiCompareMouse genome mm9 blacklisted regions — mm9_blacklist • EpiCompare - +
    @@ -32,7 +32,7 @@
    • - +

    Mouse genome mm9 blacklisted regions

    - Source: R/data.R + Source: R/data.R
    -

    Blaklisted regions of the mm9 genome build +

    Blaklisted regions of the mm9 genome build btained by lifting over the mm10_blacklist.

    @@ -84,9 +84,9 @@

    Source

    tmp <- base::get("mm10_blacklist", asNamespace("EpiCompare")) mm9_blacklist <- liftover_grlist(grlist = tmp, input_build = "mm10", - output_build = "mm9", + output_build = "mm9", keep_chr = NULL) -usethis::use_data(mm9_blacklist, overwrite = TRUE) +usethis::use_data(mm9_blacklist, overwrite = TRUE)

    @@ -98,19 +98,19 @@

    Source

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/overlap_heatmap.html b/reference/overlap_heatmap.html index 795e311..13736f5 100644 --- a/reference/overlap_heatmap.html +++ b/reference/overlap_heatmap.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Generate heatmap of percentage overlap

    - Source: R/overlap_heatmap.R + Source: R/overlap_heatmap.R
    @@ -82,35 +82,35 @@

    Generate heatmap of percentage overlap

    Arguments

    -
    peaklist
    + + +
    peaklist

    A list of peak files as GRanges object. Files must be listed and named using list(). e.g. list("name1"=file1, "name2"=file2). If not named, default file names will be assigned.

    -
    interact
    +
    interact

    Default TRUE. By default heatmap is interactive. If FALSE, heatmap is static.

    -
    draw_cellnote
    +
    draw_cellnote

    Draw the numeric values within each heatmap cell.

    -
    fill_diag
    +
    fill_diag

    Fill the diagonal of the overlap matrix.

    -
    verbose
    +
    verbose

    Print messages.

    Value

    - - -

    An interactive heatmap

    +

    An interactive heatmap

    @@ -125,7 +125,7 @@

    Examples

    #> --- Running overlap_heatmap() --- #> Warning: fill_diag must =NULL due to a known bug in the package 'heatmaply'. #> Genreating precision-recall matrix. -#> overlap_heatmap(): Done in 2.2s. +#> overlap_heatmap(): Done in 2.1s.
    @@ -136,19 +136,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/overlap_percent.html b/reference/overlap_percent.html index 9b43a95..14c070b 100644 --- a/reference/overlap_percent.html +++ b/reference/overlap_percent.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Calculate percentage of overlapping peaks

    - Source: R/overlap_percent.R + Source: R/overlap_percent.R
    @@ -82,39 +82,39 @@

    Calculate percentage of overlapping peaks

    Arguments

    -
    peaklist1
    + + +
    peaklist1

    A list of peak files as GRanges object. Files must be listed and named using list(). e.g. list("name1"=file1, "name2"=file2). If not named, default file names will be assigned.

    -
    peaklist2
    +
    peaklist2

    peaklist1 A list of peak files as GRanges object. Files must be listed and named using list(). e.g. list("name1"=file1, "name2"=file2).

    -
    invert
    +
    invert

    If TRUE, keep only the ranges in x that do not overlap ranges.

    -
    precision_recall
    -

    Return percision-recall results for all combinations -of peaklist1 (the "query") and peaklist2 (the "subject"). +

    precision_recall
    +

    Return percision-recall results for all combinations +of peaklist1 (the "query") and peaklist2 (the "subject"). See subsetByOverlaps for more details on this terminology.

    -
    suppress_messages
    +
    suppress_messages

    Suppress messages.

    Value

    - - -

    data frame

    +

    data frame

    @@ -142,19 +142,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/overlap_stat_plot.html b/reference/overlap_stat_plot.html index 78da077..2306a55 100644 --- a/reference/overlap_stat_plot.html +++ b/reference/overlap_stat_plot.html @@ -2,9 +2,9 @@ Statistical significance of overlapping peaks — overlap_stat_plot • EpiCompare - +
    @@ -40,7 +40,7 @@
    • - +

    Statistical significance of overlapping peaks

    - Source: R/overlap_stat_plot.R + Source: R/overlap_stat_plot.R
    @@ -77,9 +77,9 @@

    Statistical significance of overlapping peaks

    This function calculates the statistical significance of overlapping/ non-overlapping peaks against a reference peak file. If the reference peak file has the BED6+4 format (peak called by MACS2), the function generates a -series of box plots showing the distribution of q-values for sample peaks -that are overlapping and non-overlapping with the reference. -If the reference peak file does not have the BED6+4 format, the function uses +series of box plots showing the distribution of q-values for sample peaks +that are overlapping and non-overlapping with the reference. +If the reference peak file does not have the BED6+4 format, the function uses enrichPeakOverlap from ChIPseeker package to calculate the statistical significance of overlapping peaks only. In this case, please provide an annotation file as @@ -100,46 +100,46 @@

    Statistical significance of overlapping peaks

    Arguments

    -
    reference
    + + +
    reference

    A reference peak file as GRanges object.

    -
    peaklist
    +
    peaklist

    A list of peak files as GRanges object. Files must be listed and named using list(). E.g. list("name1"=file1, "name2"=file2). If not named, default file names will be assigned.

    -
    txdb
    +
    txdb

    A TxDb annotation object from Bioconductor. This is required only if the reference file does not have BED6+4 format.

    -
    interact
    +
    interact

    Default TRUE. By default, plots are interactive. If set FALSE, all plots in the report will be static.

    -
    nShuffle
    +
    nShuffle

    shuffle numbers

    -
    digits
    +
    digits

    integer indicating the number of decimal places (round) or significant digits (signif) to be used. For round, negative values are allowed (see ‘Details’).

    -
    workers
    +
    workers

    Number of threads to parallelize across.

    Value

    - - -

    A named list.

    • "plot"boxplot/barplot showing the statistical significance of +

      A named list.

      • "plot"boxplot/barplot showing the statistical significance of overlapping/non-overlapping peaks.

      • "data"Plot data.

    @@ -170,19 +170,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/overlap_upset_plot.html b/reference/overlap_upset_plot.html index a82db0a..635d023 100644 --- a/reference/overlap_upset_plot.html +++ b/reference/overlap_upset_plot.html @@ -1,12 +1,12 @@ Generate Upset plot for overlapping peaks — overlap_upset_plot • EpiCompare - +
    @@ -34,7 +34,7 @@
    • - +

    Generate Upset plot for overlapping peaks

    - Source: R/overlap_upset_plot.R + Source: R/overlap_upset_plot.R

    This function generates upset plot of overlapping peaks files -using the +using the ComplexUpset package.

    @@ -80,22 +80,22 @@

    Generate Upset plot for overlapping peaks

    Arguments

    -
    peaklist
    + + +
    peaklist

    A named list of peak files as GRanges object. Objects must be listed and named using list(). e.g. list("name1"=file1, "name2"=file2). If not named, default file names are assigned.

    -
    verbose
    +
    verbose

    Print messages

    Value

    - - -

    Upset plot of overlapping peaks.

    +

    Upset plot of overlapping peaks.

    @@ -106,7 +106,7 @@

    Examples

    peaklist <- list("encode"=encode_H3K27ac, "CnT"=CnT_H3K27ac) my_plot <- overlap_upset_plot(peaklist = peaklist) #> --- Running overlap_upset_plot() --- -#> overlap_upset_plot(): Done in 0.2s. +#> overlap_upset_plot(): Done in 0.3s.
    @@ -117,19 +117,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/peak_info.html b/reference/peak_info.html index e647279..533c98c 100644 --- a/reference/peak_info.html +++ b/reference/peak_info.html @@ -5,7 +5,7 @@ - +
    @@ -33,7 +33,7 @@
    • - +

    Summary of Peak Information

    - Source: R/peak_info.R + Source: R/peak_info.R
    @@ -78,20 +78,20 @@

    Summary of Peak Information

    Arguments

    -
    peaklist
    + + +
    peaklist

    A named list of peak files as GRanges object. Objects listed using list("name1" = peak, "name2" = peak2).

    -
    blacklist
    +
    blacklist

    A GRanges object containing blacklisted regions.

    Value

    - - -

    A summary table of peak information

    +

    A summary table of peak information

    @@ -119,19 +119,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/plot_ChIPseeker_annotation.html b/reference/plot_ChIPseeker_annotation.html index 1897fde..85ce229 100644 --- a/reference/plot_ChIPseeker_annotation.html +++ b/reference/plot_ChIPseeker_annotation.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Create ChIPseeker annotation plot

    - Source: R/plot_ChIPseeker_annotation.R + Source: R/plot_ChIPseeker_annotation.R
    @@ -81,34 +81,34 @@

    Create ChIPseeker annotation plot

    Arguments

    -
    peaklist
    + + +
    peaklist

    A list of peak files as GRanges object. Files must be listed and named using list(). e.g. list("name1"=file1, "name2"=file2). If not named, default file names will be assigned.

    -
    txdb
    +
    txdb

    A TxDb annotation object from Bioconductor.

    -
    tss_distance
    +
    tss_distance

    A vector specifying the distance upstream and downstream -around transcription start sites (TSS). -The default value is c(-3000,3000); meaning peak frequency +around transcription start sites (TSS). +The default value is c(-3000,3000); meaning peak frequency 3000bp upstream and downstream of TSS will be displayed.

    -
    interact
    +
    interact

    Default TRUE. By default, plots are interactive. If set FALSE, all plots in the report will be static.

    Value

    - - -

    ggplot barplot

    +

    ggplot barplot

    @@ -133,19 +133,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/plot_chromHMM.html b/reference/plot_chromHMM.html index d92a0b4..c4659f1 100644 --- a/reference/plot_chromHMM.html +++ b/reference/plot_chromHMM.html @@ -7,7 +7,7 @@ - +
    @@ -35,7 +35,7 @@
    • - +

    Plot ChromHMM heatmap

    - Source: R/plot_chromHMM.R + Source: R/plot_chromHMM.R
    @@ -89,41 +89,41 @@

    Plot ChromHMM heatmap

    Arguments

    -
    peaklist
    + + +
    peaklist

    A named list of peak files as GRanges object. If list is not named, default names will be assigned.

    -
    chromHMM_annotation
    +
    chromHMM_annotation

    ChromHMM annotation list.

    -
    genome_build
    +
    genome_build

    The human genome reference build used to generate peakfiles. "hg19" or "hg38".

    -
    cell_line
    +
    cell_line

    If not cell_line, will replace chromHMM_annotation by importing chromHMM data for a given cell line using get_chromHMM_annotation.

    -
    interact
    +
    interact

    Default TRUE. By default, the heatmaps are interactive. IfFALSE, the function generates a static ChromHMM heatmap.

    -
    return_data
    +
    return_data

    Return the plot data as in addition to the plot itself.

    Value

    - - -

    ChromHMM heatmap, or a named list.

    +

    ChromHMM heatmap, or a named list.

    @@ -166,19 +166,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/plot_corr-1.png b/reference/plot_corr-1.png index d30cb20..f2db174 100644 Binary files a/reference/plot_corr-1.png and b/reference/plot_corr-1.png differ diff --git a/reference/plot_corr.html b/reference/plot_corr.html index e843f2f..251ec98 100644 --- a/reference/plot_corr.html +++ b/reference/plot_corr.html @@ -1,11 +1,11 @@ Plot correlation of peak files — plot_corr • EpiCompare - +
    @@ -33,7 +33,7 @@
    • - +

    Plot correlation of peak files

    - Source: R/plot_corr.R + Source: R/plot_corr.R

    Plot correlation by binning genome and measuring correlation of peak quantile -ranking. This ranking is based on p-value or other peak intensity measure +ranking. This ranking is based on p-value or other peak intensity measure dependent on the peak calling approach.

    @@ -93,7 +93,9 @@

    Plot correlation of peak files

    Arguments

    -
    peakfiles
    + + +
    peakfiles

    A list of peak files as GRanges object and/or as paths to BED files. If paths are provided, EpiCompare imports the file as GRanges object. EpiCompare also accepts a list containing a mix of GRanges objects @@ -102,7 +104,7 @@

    Arguments

    default file names will be assigned.

    -
    reference
    +
    reference

    A named list containing reference peak file(s) as GRanges object. Please ensure that the reference file is listed and named i.e. list("reference_name" = reference_peak). If more than one @@ -113,82 +115,80 @@

    Arguments

    (2) ChromHMM of overlapping/non-overlapping peaks.

    -
    genome_build
    -

    The build of **all** peak and reference files to -calculate the correlation matrix on. If all peak and reference files are not -of the same build use +

    genome_build
    +

    The build of **all** peak and reference files to +calculate the correlation matrix on. If all peak and reference files are not +of the same build use liftover_grlist to convert them all before running. Genome build should be one of hg19, hg38, mm9, mm10.

    -
    bin_size
    +
    bin_size

    Default of 100. Base-pair size of the bins created to measure -correlation. Use smaller value for higher resolution but longer run time and +correlation. Use smaller value for higher resolution but longer run time and larger memory usage.

    -
    keep_chr
    +
    keep_chr

    Which chromosomes to keep.

    -
    drop_empty_chr
    -

    Drop chromosomes that are not present in any of the +

    drop_empty_chr
    +

    Drop chromosomes that are not present in any of the peakfiles (default: FALSE).

    -
    method
    -

    Default spearman (i.e. non-parametric). A character string -indicating which correlation coefficient (or covariance) is to be computed. +

    method
    +

    Default spearman (i.e. non-parametric). A character string +indicating which correlation coefficient (or covariance) is to be computed. One of "pearson", "kendall", or "spearman": can be abbreviated.

    -
    intensity_cols
    +
    intensity_cols

    Depending on which columns are present, this -value will be used to get quantiles and ultimately calculate the -correlations:

    • "total_signal" : Used by the peak calling software - SEACR. - NOTE: Another SEACR column (e.g. "max_signal") can be used +value will be used to get quantiles and ultimately calculate the +correlations:

      • "total_signal" : Used by the peak calling software + SEACR. + NOTE: Another SEACR column (e.g. "max_signal") can be used together or instead of "total_signal".

        • -

      • "qValue"Used by the peak calling software - MACS2/3. - Should contain the negative log of the p-values after multiple +

      • "qValue"Used by the peak calling software + MACS2/3. + Should contain the negative log of the p-values after multiple testing correction.

        • -

      • "Peak Score" : +

      • "Peak Score" : Used by the peak calling software HOMER.

    -
    interact
    +
    interact

    Default TRUE. By default heatmap is interactive. If FALSE, heatmap is static.

    -
    draw_cellnote
    +
    draw_cellnote

    Draw the numeric values within each heatmap cell.

    -
    fill_diag
    +
    fill_diag

    Fill the diagonal of the overlap matrix.

    -
    workers
    +
    workers

    Number of threads to parallelize across.

    -
    show_plot
    +
    show_plot

    Show the plot.

    -
    save_path
    +
    save_path

    Path to save a table of correlation results to.

    Value

    - - -

    list with correlation plot (corr_plot) and correlation matrix (data)

    +

    list with correlation plot (corr_plot) and correlation matrix (data)

    @@ -210,8 +210,8 @@

    Examples

    #> Binned matrix size: 647,114 x 3 #> Matrix sparsity: 0.996 #> Calculating correlation matrix. -#> Done computing correlations in 6 seconds. -#> Saving correlation results ==> /tmp/Rtmp2pySPs/file82a44b5a1f1c.corr.csv.gz +#> Done computing correlations in 3 seconds. +#> Saving correlation results ==> /tmp/RtmpKu2U4A/file443031d37278.corr.csv.gz
    @@ -223,19 +223,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/plot_enrichment.html b/reference/plot_enrichment.html index 4a22dd1..8ded42c 100644 --- a/reference/plot_enrichment.html +++ b/reference/plot_enrichment.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Generate enrichment analysis plots

    - Source: R/plot_enrichment.R + Source: R/plot_enrichment.R
    @@ -83,43 +83,43 @@

    Generate enrichment analysis plots

    Arguments

    -
    peaklist
    + + +
    peaklist

    A list of peak files as GRanges object. Files must be listed and named using list(). e.g. list("name1"=file1, "name2"=file2). If not named, default file names will be assigned.

    -
    txdb
    +
    txdb

    A TxDb annotation object from Bioconductor.

    -
    tss_distance
    +
    tss_distance

    A vector specifying the distance upstream and downstream -around transcription start sites (TSS). -The default value is c(-3000,3000); meaning peak frequency +around transcription start sites (TSS). +The default value is c(-3000,3000); meaning peak frequency 3000bp upstream and downstream of TSS will be displayed.

    -
    pvalueCutoff
    +
    pvalueCutoff

    P-value cutoff, passed to compareCluster.

    -
    interact
    +
    interact

    Default TRUE. By default, plots are interactive. If set FALSE, all plots in the report will be static.

    -
    verbose
    +
    verbose

    Print messages.

    Value

    - - -

    KEGG and GO dot plots

    +

    KEGG and GO dot plots

    @@ -137,7 +137,7 @@

    Examples

    #> Warning: >> TxDb is not specified, use 'TxDb.Hsapiens.UCSC.hg19.knownGene' by default... #> + Running clusterProfiler::compareCluster for KEGG. #> + Running clusterProfiler::compareCluster for GO. -#> plot_enrichment(): Done in 20s. +#> plot_enrichment(): Done in 19.7s.
    @@ -148,19 +148,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/plot_precision_recall-1.png b/reference/plot_precision_recall-1.png index 79c179a..0c69d22 100644 Binary files a/reference/plot_precision_recall-1.png and b/reference/plot_precision_recall-1.png differ diff --git a/reference/plot_precision_recall-2.png b/reference/plot_precision_recall-2.png index 60bbfbf..20fb52f 100644 Binary files a/reference/plot_precision_recall-2.png and b/reference/plot_precision_recall-2.png differ diff --git a/reference/plot_precision_recall.html b/reference/plot_precision_recall.html index 4dc5e5d..94689c3 100644 --- a/reference/plot_precision_recall.html +++ b/reference/plot_precision_recall.html @@ -1,22 +1,22 @@ -Plot precision-recall curves — plot_precision_recall • EpiCompare - +
    @@ -44,7 +44,7 @@
    • - +

    Plot precision-recall curves

    - Source: R/plot_precision_recall.R + Source: R/plot_precision_recall.R
    -

    Plot precision-recall curves (and optionally F1 plots) by -iteratively testing for peak overlap across a series of -thresholds used to filter peakfiles. +

    Plot precision-recall curves (and optionally F1 plots) by +iteratively testing for peak overlap across a series of +thresholds used to filter peakfiles. Each GRanges - object in peakfiles will be used as the "query" + object in peakfiles will be used as the "query" against each GRanges object in reference as the subject. Will automatically use any columns that are - specified with thresholding_cols and present within each - GRanges object - to create percentiles for thresholding. + specified with thresholding_cols and present within each + GRanges object + to create percentiles for thresholding. NOTE : Assumes that all GRanges in -peakfiles and reference are already +peakfiles and reference are already aligned to the same genome build.

    @@ -117,7 +117,9 @@

    Plot precision-recall curves

    Arguments

    -
    peakfiles
    + + +
    peakfiles

    A list of peak files as GRanges object and/or as paths to BED files. If paths are provided, EpiCompare imports the file as GRanges object. EpiCompare also accepts a list containing a mix of GRanges objects @@ -126,7 +128,7 @@

    Arguments

    default file names will be assigned.

    -
    reference
    +
    reference

    A named list containing reference peak file(s) as GRanges object. Please ensure that the reference file is listed and named i.e. list("reference_name" = reference_peak). If more than one @@ -137,84 +139,82 @@

    Arguments

    (2) ChromHMM of overlapping/non-overlapping peaks.

    -
    thresholding_cols
    -

    Depending on which columns are present, - GRanges will - be filtered at each threshold according to one or more of the following:

    • "total_signal" : Used by the peak calling software - SEACR. - NOTE: Another SEACR column (e.g. "max_signal") can be used +

      thresholding_cols
      +

      Depending on which columns are present, + GRanges will + be filtered at each threshold according to one or more of the following:

      • "total_signal" : Used by the peak calling software + SEACR. + NOTE: Another SEACR column (e.g. "max_signal") can be used together or instead of "total_signal".

        • -

      • "qValue"Used by the peak calling software - MACS2/3. - Should contain the negative log of the p-values after multiple +

      • "qValue"Used by the peak calling software + MACS2/3. + Should contain the negative log of the p-values after multiple testing correction.

        • -

      • "Peak Score" : +

      • "Peak Score" : Used by the peak calling software HOMER.

      -
      initial_threshold
      -

      Numeric threshold that was provided to SEACR -(via the parameter --ctrl) when calling peaks without an IgG +

      initial_threshold
      +

      Numeric threshold that was provided to SEACR +(via the parameter --ctrl) when calling peaks without an IgG control.

      -
      n_threshold
      +
      n_threshold

      Number of thresholds to test.

      -
      max_threshold
      +
      max_threshold

      Maximum threshold to test.

      -
      workers
      +
      workers

      Number of threads to parallelize across.

      -
      plot_f1
      +
      plot_f1

      Generate a plot with the F1 score vs. threshold as well.

      -
      subtitle
      +
      subtitle

      Plot subtitle.

      -
      color
      +
      color

      Variable to color data points by.

      -
      shape
      +
      shape

      Variable to set data point shapes by.

      -
      facets
      +
      facets

      [Deprecated] Please use rows and cols instead.

      -
      interact
      +
      interact

      Default TRUE. By default, plots are interactive. If set FALSE, all plots in the report will be static.

      -
      show_plot
      +
      show_plot

      Show the plot.

      -
      save_path
      +
      save_path

      File path to save precision-recall results to.

      -
      verbose
      +
      verbose

      Print messages.

    Value

    - - -

    list with data and precision recall and F1 plots

    +

    list with data and precision recall and F1 plots

    @@ -229,7 +229,7 @@

    Examples

    reference = reference, workers = 1) #> Reformatting precision-recall data. -#> Saving precision-recall results ==> /tmp/Rtmp2pySPs/file82a45317cbdaprecision_recall.csv +#> Saving precision-recall results ==> /tmp/RtmpKu2U4A/file44301f727402precision_recall.csv #> Plotting precision-recall curve. #> Warning: The `facets` argument of `facet_grid()` is deprecated as of ggplot2 2.2.0. #> ℹ Please use the `rows` argument instead. @@ -249,19 +249,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/precision_recall.html b/reference/precision_recall.html index 7648bbc..24f5c72 100644 --- a/reference/precision_recall.html +++ b/reference/precision_recall.html @@ -1,12 +1,12 @@ Compute precision-recall — precision_recall • EpiCompare - +
    @@ -34,7 +34,7 @@
    • - +

    Compute precision-recall

    - Source: R/precision_recall.R + Source: R/precision_recall.R

    Compute precision and recall using each GRanges - object in peakfiles as the "query" + object in peakfiles as the "query" against each GRanges object in reference as the subject.

    @@ -92,7 +92,9 @@

    Compute precision-recall

    Arguments

    -
    peakfiles
    + + +
    peakfiles

    A list of peak files as GRanges object and/or as paths to BED files. If paths are provided, EpiCompare imports the file as GRanges object. EpiCompare also accepts a list containing a mix of GRanges objects @@ -101,7 +103,7 @@

    Arguments

    default file names will be assigned.

    -
    reference
    +
    reference

    A named list containing reference peak file(s) as GRanges object. Please ensure that the reference file is listed and named i.e. list("reference_name" = reference_peak). If more than one @@ -112,55 +114,55 @@

    Arguments

    (2) ChromHMM of overlapping/non-overlapping peaks.

    -
    thresholding_cols
    -

    Depending on which columns are present, - GRanges will - be filtered at each threshold according to one or more of the following:

    • "total_signal" : Used by the peak calling software - SEACR. - NOTE: Another SEACR column (e.g. "max_signal") can be used +

      thresholding_cols
      +

      Depending on which columns are present, + GRanges will + be filtered at each threshold according to one or more of the following:

      • "total_signal" : Used by the peak calling software + SEACR. + NOTE: Another SEACR column (e.g. "max_signal") can be used together or instead of "total_signal".

        • -

      • "qValue"Used by the peak calling software - MACS2/3. - Should contain the negative log of the p-values after multiple +

      • "qValue"Used by the peak calling software + MACS2/3. + Should contain the negative log of the p-values after multiple testing correction.

        • -

      • "Peak Score" : +

      • "Peak Score" : Used by the peak calling software HOMER.

      -
      initial_threshold
      -

      Numeric threshold that was provided to SEACR -(via the parameter --ctrl) when calling peaks without an IgG +

      initial_threshold
      +

      Numeric threshold that was provided to SEACR +(via the parameter --ctrl) when calling peaks without an IgG control.

      -
      n_threshold
      +
      n_threshold

      Number of thresholds to test.

      -
      max_threshold
      +
      max_threshold

      Maximum threshold to test.

      -
      cast
      -

      Cast the data into a format that's more compatible with +

      cast
      +

      Cast the data into a format that's more compatible with ggplot2.

      -
      workers
      +
      workers

      Number of threads to parallelize across.

      -
      verbose
      +
      verbose

      Print messages.

      -
      save_path
      +
      save_path

      File path to save precision-recall results to.

      -
      ...
      +
      ...

      Arguments passed on to bpplapply

      apply_fun

      Iterator function to use.

      @@ -185,15 +187,13 @@

      Arguments

      FUN

      The function to be applied to each element of X.

      - +

    Value

    - - -

    Overlap

    +

    Overlap

    @@ -208,7 +208,7 @@

    Examples

    reference = reference, workers = 1) #> Reformatting precision-recall data. -#> Saving precision-recall results ==> /tmp/Rtmp2pySPs/file82a469a9dcb5precision_recall.csv +#> Saving precision-recall results ==> /tmp/RtmpKu2U4A/file443069f1precision_recall.csv
    @@ -219,19 +219,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/precision_recall_matrix.html b/reference/precision_recall_matrix.html index 3cdd5e3..595f11a 100644 --- a/reference/precision_recall_matrix.html +++ b/reference/precision_recall_matrix.html @@ -1,10 +1,10 @@ -Create a precision-recall matrix — precision_recall_matrix • EpiCompareCreate a precision-recall matrix — precision_recall_matrix • EpiCompare - +
    @@ -32,7 +32,7 @@
    • - +

    Create a precision-recall matrix

    - Source: R/precision_recall_matrix.R + Source: R/precision_recall_matrix.R
    -

    Converts a list of peak files to a symmetric matrix where +

    Converts a list of peak files to a symmetric matrix where the y-axis indicates precision and the x-axis indicates recall.

    @@ -76,19 +76,19 @@

    Create a precision-recall matrix

    Arguments

    -
    fill_diag
    + + +
    fill_diag

    Fill the diagonal of the overlap matrix.

    -
    verbose
    +
    verbose

    Print messages.

    Value

    - - -

    matrix

    +

    matrix

    @@ -99,19 +99,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/predict_precision_recall.html b/reference/predict_precision_recall.html index 40eafa5..304c964 100644 --- a/reference/predict_precision_recall.html +++ b/reference/predict_precision_recall.html @@ -1,12 +1,12 @@ Predict precision-recall — predict_precision_recall • EpiCompare - +
    @@ -34,7 +34,7 @@
    • - +

    Predict precision-recall

    - Source: R/predict_precision_recall.R + Source: R/predict_precision_recall.R

    Predict specific values of precision or recall by fitting a model to -a precision-recall curve. +a precision-recall curve. Predictions that are <0 will automatically be set to 0. Predictions that are >100 will automatically be set to 100.

    @@ -90,28 +90,28 @@

    Source

    Arguments

    -
    pr_df
    -

    Precision-recall data.frame generated by + + +

    pr_df
    +

    Precision-recall data.frame generated by precision_recall.

    -
    fun
    +
    fun

    Function to fit the data with.

    -
    precision
    +
    precision

    Precision values to predict recall from.

    -
    recall
    +
    recall

    Recall values to predict precision from.

    Value

    - - -

    A named list of fitted models and predictions.

    +

    A named list of fitted models and predictions.

    @@ -124,7 +124,7 @@

    Examples

    pr_df <- precision_recall(peakfiles = peakfiles, reference = reference) #> Reformatting precision-recall data. -#> Saving precision-recall results ==> /tmp/Rtmp2pySPs/file82a42cee227precision_recall.csv +#> Saving precision-recall results ==> /tmp/RtmpKu2U4A/file44304df69adbprecision_recall.csv predictions <- predict_precision_recall(pr_df = pr_df) #> Making predictions for peaklist1: CnR_H3K27ac #> Making predictions for peaklist2: encode_H3K27ac @@ -144,19 +144,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/predict_values.html b/reference/predict_values.html index bab6fc2..bb4bdf9 100644 --- a/reference/predict_values.html +++ b/reference/predict_values.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Predict values

    - Source: R/predict_values.R + Source: R/predict_values.R
    @@ -74,31 +74,31 @@

    Predict values

    Arguments

    -
    df
    + + +
    df

    data.frame

    -
    fun
    +
    fun

    Function to fit the data with.

    -
    values
    +
    values

    Values to make predictions from.

    -
    input_var
    +
    input_var

    Input variable column name.

    -
    predicted_var
    +
    predicted_var

    Predicted variable name.

    Value

    - - -

    data.frame

    +

    data.frame

    @@ -109,19 +109,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/prepare_blacklist.html b/reference/prepare_blacklist.html index 69460a3..8b6b9ff 100644 --- a/reference/prepare_blacklist.html +++ b/reference/prepare_blacklist.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Prepare blacklist as GRanges

    - Source: R/prepare_blacklist.R + Source: R/prepare_blacklist.R
    @@ -79,26 +79,26 @@

    Prepare blacklist as GRanges

    Arguments

    -
    output_build
    + + +
    output_build

    Desired genome build for grlist to be lifted over to.

    -
    blacklist_build
    +
    blacklist_build

    Genome build of the blacklist. -Only used when blacklist is a user-supplied +Only used when blacklist is a user-supplied GRanges object.

    -
    verbose
    +
    verbose

    Print messages.

    Value

    - - -

    A GRanges objects of blacklisted +

    A GRanges objects of blacklisted genomic regions from the relevant genome build.

    @@ -110,19 +110,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/prepare_genome_builds.html b/reference/prepare_genome_builds.html index 885606b..b7b63e8 100644 --- a/reference/prepare_genome_builds.html +++ b/reference/prepare_genome_builds.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Prepare genome builds

    - Source: R/prepare_genome_builds.R + Source: R/prepare_genome_builds.R
    @@ -76,7 +76,9 @@

    Prepare genome builds

    Arguments

    -
    genome_build
    + + +
    genome_build

    A named list indicating the human genome build used to generate each of the following inputs:

    • "peakfiles" : Genome build for the peakfiles input. Assumes genome build is the same for each element in the peakfiles @@ -91,7 +93,7 @@

      Arguments

      genome build. For example:
      genome_build = "hg19"

    -
    blacklist
    +
    blacklist

    A GRanges object containing blacklisted genomic regions. Blacklists included in EpiCompare are:

    • NULL (default): Automatically selects the appropriate @@ -103,18 +105,16 @@

      Arguments

    • "mm10_blacklist": Regions of mm10 genome that have anomalous and/or unstructured signals. mm10_blacklist

    • "mm9_blacklist": Blacklisted regions of mm10 genome that have been - lifted over from mm10_blacklist. + lifted over from mm10_blacklist. mm9_blacklist

      • -

    • <user_input>: A custom user-provided blacklist in +

    • <user_input>: A custom user-provided blacklist in GRanges format.

    Value

    - - -

    Named list.

    +

    Named list.

    @@ -125,19 +125,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/prepare_peaklist.html b/reference/prepare_peaklist.html index 1bd9a9d..8931737 100644 --- a/reference/prepare_peaklist.html +++ b/reference/prepare_peaklist.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Prepare peaklist as GRanges

    - Source: R/prepare_peaklist.R + Source: R/prepare_peaklist.R
    @@ -74,25 +74,25 @@

    Prepare peaklist as GRanges

    Arguments

    -
    peaklist
    + + +
    peaklist

    A named list of peaks as GRanges or paths to BED files.

    -
    remove_empty
    +
    remove_empty

    Remove any empty elements in the list.

    -
    as_grangeslist
    +
    as_grangeslist

    Convert output to class GRangesList before returning.

    Value

    - - -

    A list of GRanges objects

    +

    A list of GRanges objects

    @@ -103,19 +103,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/prepare_reference.html b/reference/prepare_reference.html index e68987d..4465e6c 100644 --- a/reference/prepare_reference.html +++ b/reference/prepare_reference.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Prepare referemce as GRanges

    - Source: R/prepare_reference.R + Source: R/prepare_reference.R
    @@ -80,35 +80,35 @@

    Prepare referemce as GRanges

    Arguments

    -
    reference
    -

    A named list of GRanges objects, -or a single GRanges object to be converted into a + + +

    reference
    +

    A named list of GRanges objects, +or a single GRanges object to be converted into a named list.

    -
    max_elements
    +
    max_elements

    Max number of elements to use within the list. Set to NULL (default) to use all elements.

    -
    remove_empty
    +
    remove_empty

    Remove any empty elements in the list.

    -
    as_list
    +
    as_list

    Return as a list.

    -
    as_grangeslist
    +
    as_grangeslist

    Return as a GRangesList (overrides as_list).

    Value

    - - -

    A list of GRanges objects

    +

    A list of GRanges objects

    @@ -119,19 +119,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/read_bowtie.html b/reference/read_bowtie.html index 881f9b9..6681bf9 100644 --- a/reference/read_bowtie.html +++ b/reference/read_bowtie.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Read bowtie

    - Source: R/read_bowtie.R + Source: R/read_bowtie.R
    @@ -74,21 +74,19 @@

    Read bowtie

    Arguments

    -
    path
    + + +
    path

    Path to bowtie file.

    -
    verbose
    +
    verbose

    Print messages.

    Value

    - - -

    data.table

    - - +

    data.table

    @@ -99,19 +97,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/read_peaks.html b/reference/read_peaks.html index 9150394..b1a0d54 100644 --- a/reference/read_peaks.html +++ b/reference/read_peaks.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Read peaks

    - Source: R/read_peaks.R + Source: R/read_peaks.R
    @@ -74,11 +74,13 @@

    Read peaks

    Arguments

    -
    path
    + + +
    path

    Path to peak file.

    -
    type
    +
    type

    File type to search for. Options include:

    • "<pattern>"Finds files matching an arbitrary regex pattern specified by user.

    • "peaks.stringent"Finds files ending in "*.stringent.bed$"

      • @@ -90,17 +92,13 @@

      Arguments

    -
    verbose
    +
    verbose

    Print messages.

    Value

    - - -

    GRanges

    - - +

    GRanges

    @@ -111,19 +109,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/rebin_peaks.html b/reference/rebin_peaks.html index 00819fd..402e4eb 100644 --- a/reference/rebin_peaks.html +++ b/reference/rebin_peaks.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Rebin peaks

    - Source: R/rebin_peaks.R + Source: R/rebin_peaks.R
    @@ -88,7 +88,9 @@

    Rebin peaks

    Arguments

    -
    peakfiles
    + + +
    peakfiles

    A list of peak files as GRanges object and/or as paths to BED files. If paths are provided, EpiCompare imports the file as GRanges object. EpiCompare also accepts a list containing a mix of GRanges objects @@ -97,66 +99,66 @@

    Arguments

    default file names will be assigned.

    -
    genome_build
    -

    The build of **all** peak and reference files to -calculate the correlation matrix on. If all peak and reference files are not -of the same build use +

    genome_build
    +

    The build of **all** peak and reference files to +calculate the correlation matrix on. If all peak and reference files are not +of the same build use liftover_grlist to convert them all before running. Genome build should be one of hg19, hg38, mm9, mm10.

    -
    intensity_cols
    +
    intensity_cols

    Depending on which columns are present, this -value will be used to get quantiles and ultimately calculate the -correlations:

    • "total_signal" : Used by the peak calling software - SEACR. - NOTE: Another SEACR column (e.g. "max_signal") can be used +value will be used to get quantiles and ultimately calculate the +correlations:

      • "total_signal" : Used by the peak calling software + SEACR. + NOTE: Another SEACR column (e.g. "max_signal") can be used together or instead of "total_signal".

        • -

      • "qValue"Used by the peak calling software - MACS2/3. - Should contain the negative log of the p-values after multiple +

      • "qValue"Used by the peak calling software + MACS2/3. + Should contain the negative log of the p-values after multiple testing correction.

        • -

      • "Peak Score" : +

      • "Peak Score" : Used by the peak calling software HOMER.

    -
    bin_size
    +
    bin_size

    Default of 100. Base-pair size of the bins created to measure -correlation. Use smaller value for higher resolution but longer run time and +correlation. Use smaller value for higher resolution but longer run time and larger memory usage.

    -
    keep_chr
    +
    keep_chr

    Which chromosomes to keep.

    -
    sep
    -

    Separator to be used after chromosome name (first item) and +

    sep
    +

    Separator to be used after chromosome name (first item) and between start/end genomic coordinates (second item).

    -
    drop_empty_chr
    -

    Drop chromosomes that are not present in any of the +

    drop_empty_chr
    +

    Drop chromosomes that are not present in any of the peakfiles (default: FALSE).

    -
    as_sparse
    +
    as_sparse

    Return the rebinned peaks as a sparse matrix -(default: TRUE), +(default: TRUE), which is more efficiently stored than a dense matrix (FALSE).

    -
    workers
    +
    workers

    Number of threads to parallelize across.

    -
    verbose
    +
    verbose

    Print messages.

    -
    ...
    +
    ...

    Arguments passed on to bpplapply

    apply_fun

    Iterator function to use.

    @@ -181,15 +183,13 @@

    Arguments

    FUN

    The function to be applied to each element of X.

    - +

    Value

    - - -

    Binned peaks matrix

    +

    Binned peaks matrix

    @@ -218,19 +218,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/remove_nonstandard_chrom.html b/reference/remove_nonstandard_chrom.html index b66192c..def8305 100644 --- a/reference/remove_nonstandard_chrom.html +++ b/reference/remove_nonstandard_chrom.html @@ -1,10 +1,10 @@ -Remove non-standard chromosomes — remove_nonstandard_chrom • EpiCompareRemove non-standard chromosomes — remove_nonstandard_chrom • EpiCompare - +
    @@ -32,7 +32,7 @@
    • - +

    Remove non-standard chromosomes

    - Source: R/remove_nonstandard_chrom.R + Source: R/remove_nonstandard_chrom.R
    -

    Remove non-standard chromosomes from a list of +

    Remove non-standard chromosomes from a list of GRanges objects.

    @@ -80,23 +80,23 @@

    Remove non-standard chromosomes

    Arguments

    -
    grlist
    + + +
    grlist

    Named list of GRanges objects.

    -
    keep_chr
    +
    keep_chr

    Which chromosomes to keep.

    -
    verbose
    +
    verbose

    Print messages.

    Value

    - - -

    Named list of GRanges objects.

    +

    Named list of GRanges objects.

    @@ -107,19 +107,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/report_command.html b/reference/report_command.html index 9ca12a1..8c0722f 100644 --- a/reference/report_command.html +++ b/reference/report_command.html @@ -1,10 +1,10 @@ -Report command — report_command • EpiCompareReport command — report_command • EpiCompare - +
    @@ -32,7 +32,7 @@
    • - +

    Report command

    - Source: R/report_command.R + Source: R/report_command.R
    -

    Reconstruct the EpiCompare command +

    Reconstruct the EpiCompare command used to generate the current Rmarkdown report.

    @@ -76,29 +76,28 @@

    Report command

    Arguments

    -
    params
    + + +
    params

    Parameters supplied to the Rmarkdown template.

    -
    peaklist_tidy
    +
    peaklist_tidy

    Post-processed target peaks.

    -
    reference_tidy
    +
    reference_tidy

    Post-processed reference peaks.

    Value

    - - -

    String reconstructing R function call.

    +

    String reconstructing R function call.

    Examples

    # report_command()
-
    @@ -109,19 +108,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/report_header.html b/reference/report_header.html index 8fbb1bc..cc7cebe 100644 --- a/reference/report_header.html +++ b/reference/report_header.html @@ -1,10 +1,10 @@ -Report header — report_header • EpiCompareReport header — report_header • EpiCompare - +
    @@ -32,7 +32,7 @@
    • - +

    Report header

    - Source: R/report_header.R + Source: R/report_header.R
    -

    Generate a header for EpiCompare reports generated using +

    Generate a header for EpiCompare reports generated using the EpiCompare.Rmd template.

    @@ -76,9 +76,7 @@

    Report header

    Value

    - - -

    Header string to be rendering within Rmarkdown file.

    +

    Header string to be rendering within Rmarkdown file.

    @@ -95,19 +93,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/save_output.html b/reference/save_output.html index 50abc48..f80930f 100644 --- a/reference/save_output.html +++ b/reference/save_output.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Save output

    - Source: R/save_output.R + Source: R/save_output.R
    @@ -82,41 +82,41 @@

    Save output

    Arguments

    -
    save_output
    + + +
    save_output

    Default FALSE. If TRUE, outputs are saved.

    -
    file
    +
    file

    Tables and plots to be saved.

    -
    file_type
    +
    file_type

    Type of file to be saved. "data.frame", "ggplot", "image"

    -
    filename
    +
    filename

    Name of file.

    -
    outpath
    +
    outpath

    Outpath

    -
    interactive
    +
    interactive

    Default FALSE. If TRUE, interactive plots are saved as html.

    -
    verbose
    +
    verbose

    Print messages.

    Value

    - - -

    Saved data frames and plots.

    +

    Saved data frames and plots.

    @@ -127,19 +127,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/set_min_max.html b/reference/set_min_max.html index e7626aa..7970aab 100644 --- a/reference/set_min_max.html +++ b/reference/set_min_max.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Set min/max

    - Source: R/set_min_max.R + Source: R/set_min_max.R
    @@ -74,27 +74,27 @@

    Set min/max

    Arguments

    -
    df
    + + +
    df

    data.frame

    -
    colname
    +
    colname

    Column name to check.

    -
    min_val
    +
    min_val

    Minimum value.

    -
    max_val
    +
    max_val

    Maximum value.

    Value

    - - -

    data.frame

    +

    data.frame

    @@ -105,19 +105,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/stopper.html b/reference/stopper.html index 093f209..210f104 100644 --- a/reference/stopper.html +++ b/reference/stopper.html @@ -1,12 +1,12 @@ Stop messages — stopper • EpiCompare - +
    @@ -34,7 +34,7 @@
    • - +

    Stop messages

    - Source: R/stopper.R + Source: R/stopper.R

    Conditionally print stop messages. -Allows developers to easily control verbosity of functions, - and meet Bioconductor requirements that dictate the stop message +Allows developers to easily control verbosity of functions, + and meet Bioconductor requirements that dictate the stop message must first be stored to a variable before passing to stop.

    @@ -80,15 +80,15 @@

    Stop messages

    Arguments

    -
    v
    + + +
    v

    Whether to print messages or not.

    Value

    - - -

    Null

    +

    Null

    @@ -99,19 +99,19 @@

    Value

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/tidy_chromosomes.html b/reference/tidy_chromosomes.html new file mode 100644 index 0000000..913a17d --- /dev/null +++ b/reference/tidy_chromosomes.html @@ -0,0 +1,224 @@ + +Remove odd chromosomes from GRanges objects — tidy_chromosomes • EpiCompare + + +
    +
    + + + +
    +
    +
    +

    Remove odd chromosomes from GRanges objects

    + Source: R/tidy_chromosomes.R + +
    + +
    +

    This convenience function removes non-standard, mitochondrial, and/or sex +chromosomes from any GRanges object.

    +
    + +
    + 
    tidy_chromosomes(
+  gr,
+  keep.X = TRUE,
+  keep.Y = TRUE,
+  keep.M = FALSE,
+  keep.nonstandard = FALSE,
+  genome = NULL
+)
    +
    + +
    +

    Arguments

    + + +
    gr
    +

    Any GRanges object, or any another object with associated +seqinfo (or a Seqinfo object itself). The object should +typically have a standard genome associated with it, e.g. genome(gr) +<- "hg38". gr can also be a list of such GRanges objects.

    + + +
    keep.X, keep.Y, keep.M, keep.nonstandard
    +

    Logicals indicating which +non-autosomes should be kept. By default, sex chromosomes are kept, but +mitochondrial and non-standard chromosomes are removed.

    + + +
    genome
    +

    An optional string that, if supplied, will be used to set the +genome of gr.

    + +
    +
    +

    Value

    +

    A GRanges object in which both ranges and seqinfo associated + with trimmed chromosomes have been removed.

    +
    +
    +

    Details

    +

    This function is adapted from tidyChromosomes in the +BRGenomics package licensed under the Artistic License 2.0. +Original author: Mike DeBerardine <https://github.com/mdeber>

    +

    Standard chromosomes are defined using the + standardChromosomes function + from the GenomeInfoDb package.

    +
    + +
    +

    Author

    +

    Mike DeBerardine

    +
    + +
    +

    Examples

    + 
    # make a GRanges
+chrom <- c("chr2", "chr3", "chrX", "chrY", "chrM", "junk")
+gr <- GenomicRanges::GRanges(seqnames = chrom,
+              ranges = IRanges::IRanges(start = 2*(1:6), end = 3*(1:6)),
+              strand = "+",
+              seqinfo = GenomeInfoDb::Seqinfo(chrom))
+GenomeInfoDb::genome(gr) <- "hg38"
+
+gr
+#> GRanges object with 6 ranges and 0 metadata columns:
+#>       seqnames    ranges strand
+#>          <Rle> <IRanges>  <Rle>
+#>   [1]     chr2       2-3      +
+#>   [2]     chr3       4-6      +
+#>   [3]     chrX       6-9      +
+#>   [4]     chrY      8-12      +
+#>   [5]     chrM     10-15      +
+#>   [6]     junk     12-18      +
+#>   -------
+#>   seqinfo: 6 sequences from hg38 genome; no seqlengths
+
+tidy_chromosomes(gr)
+#> GRanges object with 4 ranges and 0 metadata columns:
+#>       seqnames    ranges strand
+#>          <Rle> <IRanges>  <Rle>
+#>   [1]     chr2       2-3      +
+#>   [2]     chr3       4-6      +
+#>   [3]     chrX       6-9      +
+#>   [4]     chrY      8-12      +
+#>   -------
+#>   seqinfo: 4 sequences from hg38 genome; no seqlengths
+
+tidy_chromosomes(gr, keep.M = TRUE)
+#> GRanges object with 5 ranges and 0 metadata columns:
+#>       seqnames    ranges strand
+#>          <Rle> <IRanges>  <Rle>
+#>   [1]     chr2       2-3      +
+#>   [2]     chr3       4-6      +
+#>   [3]     chrX       6-9      +
+#>   [4]     chrY      8-12      +
+#>   [5]     chrM     10-15      +
+#>   -------
+#>   seqinfo: 5 sequences from hg38 genome; no seqlengths
+
+tidy_chromosomes(gr, keep.M = TRUE, keep.Y = FALSE)
+#> GRanges object with 4 ranges and 0 metadata columns:
+#>       seqnames    ranges strand
+#>          <Rle> <IRanges>  <Rle>
+#>   [1]     chr2       2-3      +
+#>   [2]     chr3       4-6      +
+#>   [3]     chrX       6-9      +
+#>   [4]     chrM     10-15      +
+#>   -------
+#>   seqinfo: 4 sequences from hg38 genome; no seqlengths
+
+tidy_chromosomes(gr, keep.nonstandard = TRUE)
+#> GRanges object with 5 ranges and 0 metadata columns:
+#>       seqnames    ranges strand
+#>          <Rle> <IRanges>  <Rle>
+#>   [1]     chr2       2-3      +
+#>   [2]     chr3       4-6      +
+#>   [3]     chrX       6-9      +
+#>   [4]     chrY      8-12      +
+#>   [5]     junk     12-18      +
+#>   -------
+#>   seqinfo: 5 sequences from hg38 genome; no seqlengths
+
+
    +
    +
    + +
    + + +
    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    +
    + +
    +

    Site built with pkgdown 2.1.1.

    +
    + +
    + + + + + + + + diff --git a/reference/tidy_peakfile.html b/reference/tidy_peakfile.html index 032ef4b..390d19e 100644 --- a/reference/tidy_peakfile.html +++ b/reference/tidy_peakfile.html @@ -6,7 +6,7 @@ - +
    @@ -34,7 +34,7 @@
    • - +

    Tidy peakfiles in GRanges

    - Source: R/tidy_peakfile.R + Source: R/tidy_peakfile.R
    @@ -80,22 +80,22 @@

    Tidy peakfiles in GRanges

    Arguments

    -
    peaklist
    + + +
    peaklist

    A named list of peak files as GRanges object. Objects must be named and listed using list(). e.g. list("name1"=file1, "name2"=file2) If not named, default names are assigned.

    -
    blacklist
    +
    blacklist

    Peakfile specifying blacklisted regions as GRanges object.

    Value

    - - -

    list of GRanges object

    +

    list of GRanges object

    @@ -122,19 +122,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/translate_genome.html b/reference/translate_genome.html index 03a06b3..ef39bb5 100644 --- a/reference/translate_genome.html +++ b/reference/translate_genome.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Translate genome

    - Source: R/translate_genome.R + Source: R/translate_genome.R
    @@ -79,29 +79,29 @@

    Translate genome

    Arguments

    -
    genome
    + + +
    genome

    A character vector of genomes equivalent to UCSC version or Ensembl Assemblies

    -
    style
    +
    style

    A single value equivalent to "UCSC" or "Ensembl" specifying the output genome

    -
    default_genome
    +
    default_genome

    Default genome build when genome is NULL.

    -
    omit_subversion
    +
    omit_subversion

    Omit any subversion suffixes after the ".".

    Value

    - - -

    Standardized genome build name as a character string.

    +

    Standardized genome build name as a character string.

    @@ -118,19 +118,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/tss_plot.html b/reference/tss_plot.html index 04c343c..dbaded6 100644 --- a/reference/tss_plot.html +++ b/reference/tss_plot.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Read count frequency around TSS

    - Source: R/tss_plot.R + Source: R/tss_plot.R
    @@ -82,50 +82,50 @@

    Read count frequency around TSS

    Arguments

    -
    peaklist
    + + +
    peaklist

    A list of peak files as GRanges object. Files must be listed and named using list(). e.g. list("name1"=file1, "name2"=file2) If not named, default file names will be assigned.

    -
    txdb
    +
    txdb

    A TxDb annotation object from Bioconductor.

    -
    tss_distance
    +
    tss_distance

    A vector specifying the distance upstream and downstream -around transcription start sites (TSS). -The default value is c(-3000,3000); meaning peak frequency +around transcription start sites (TSS). +The default value is c(-3000,3000); meaning peak frequency 3000bp upstream and downstream of TSS will be displayed.

    -
    conf
    +
    conf

    Confidence interval threshold estimated by bootstrapping (0.95 means 95 Argument passed to plotAvgProf.

    -
    resample
    +
    resample

    Number of bootstrapped iterations to run. Argument passed to plotAvgProf.

    -
    interact
    +
    interact

    Default TRUE. By default, plots are interactive. If set FALSE, all plots in the report will be static.

    -
    workers
    +
    workers

    Number of cores to parallelise bootstrapping across. Argument passed to plotAvgProf.

    Value

    - - -

    A named list of profile plots.

    +

    A named list of profile plots.

    @@ -140,8 +140,8 @@

    Examples

    workers = 1) #> --- Running tss_plot() --- #> Warning: >> TxDb is not specified, use 'TxDb.Hsapiens.UCSC.hg19.knownGene' by default... -#> >> Running bootstrapping for tag matrix... 2024-04-25 04:07:36 PM -#> >> Running bootstrapping for tag matrix... 2024-04-25 04:07:36 PM +#> >> Running bootstrapping for tag matrix... 2024-10-18 02:21:02 PM +#> >> Running bootstrapping for tag matrix... 2024-10-18 02:21:02 PM #> Done.
    @@ -153,19 +153,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/width_boxplot.html b/reference/width_boxplot.html index 0bf5ecf..9b08303 100644 --- a/reference/width_boxplot.html +++ b/reference/width_boxplot.html @@ -4,7 +4,7 @@ - +
    @@ -32,7 +32,7 @@
    • - +

    Peak width boxplot

    - Source: R/width_boxplot.R + Source: R/width_boxplot.R
    @@ -76,22 +76,22 @@

    Peak width boxplot

    Arguments

    -
    peaklist
    + + +
    peaklist

    A list of peak files as GRanges object. Files must be named and listed using list(). e.g. list("name1"=file1, "name2"=file2)

    -
    interact
    +
    interact

    Default TRUE. By default, plots are interactive. If set FALSE, all plots in the report will be static.

    Value

    - - -

    A boxplot of peak widths.

    +

    A boxplot of peak widths.

    @@ -113,19 +113,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/write_example_peaks.html b/reference/write_example_peaks.html index 3489b95..2feb27c 100644 --- a/reference/write_example_peaks.html +++ b/reference/write_example_peaks.html @@ -3,7 +3,7 @@ - +
    @@ -31,7 +31,7 @@
    • - +

    Write example peaks

    - Source: R/write_example_peaks.R + Source: R/write_example_peaks.R
    @@ -77,27 +77,27 @@

    Write example peaks

    Arguments

    -
    dir
    + + +
    dir

    Directory to save peak files to.

    -
    datasets
    +
    datasets

    Example datasets from EpiCompare to write.

    Value

    - - -

    Named vector of paths to saved peak files.

    +

    Named vector of paths to saved peak files.

    Examples

    save_paths <- EpiCompare::write_example_peaks()
-#> Writing ==> /tmp/Rtmp2pySPs/processed_results/encode_H3K27ac.narrowPeaks.bed
-#> Writing ==> /tmp/Rtmp2pySPs/processed_results/CnT_H3K27ac.narrowPeaks.bed
-#> Writing ==> /tmp/Rtmp2pySPs/processed_results/CnR_H3K27ac.narrowPeaks.bed
+#> Writing ==> /tmp/RtmpKu2U4A/processed_results/encode_H3K27ac.narrowPeaks.bed
+#> Writing ==> /tmp/RtmpKu2U4A/processed_results/CnT_H3K27ac.narrowPeaks.bed
+#> Writing ==> /tmp/RtmpKu2U4A/processed_results/CnR_H3K27ac.narrowPeaks.bed
    @@ -108,19 +108,19 @@

    Examples

    -

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Thomas Roberts.

    +

    Developed by Sera Choi, Brian Schilder, Leyla Abbasova, Alan Murphy, Nathan Skene, Hiranyamaya Dash.

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/sitemap.xml b/sitemap.xml index 0efe5d6..7ed2626 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1,225 +1,78 @@ - - - - /404.html - - - /articles/EpiCompare.html - - - /articles/docker.html - - - /articles/example_report.html - - - /articles/index.html - - - /authors.html - - - /index.html - - - /news/index.html - - - /reference/CnR_H3K27ac.html - - - /reference/CnR_H3K27ac_picard.html - - - /reference/CnT_H3K27ac.html - - - /reference/CnT_H3K27ac_picard.html - - - /reference/EpiCompare.html - - - /reference/as_interactive.html - - - /reference/bpplapply.html - - - /reference/checkCache.html - - - /reference/check_cell_lines.html - - - /reference/check_genome_build.html - - - /reference/check_grlist_cols.html - - - /reference/check_list_names.html - - - /reference/check_workers.html - - - /reference/clean_granges.html - - - /reference/compute_consensus_peaks.html - - - /reference/compute_corr.html - - - /reference/download_button.html - - - /reference/encode_H3K27ac.html - - - /reference/fig_length.html - - - /reference/fragment_info.html - - - /reference/gather_files.html - - - /reference/gather_files_names.html - - - /reference/get_bpparam.html - - - /reference/get_chromHMM_annotation.html - - - /reference/group_files.html - - - /reference/hg19_blacklist.html - - - /reference/hg38_blacklist.html - - - /reference/index.html - - - /reference/is_granges.html - - - /reference/liftover_grlist.html - - - /reference/message_parallel.html - - - /reference/messager.html - - - /reference/mm10_blacklist.html - - - /reference/mm9_blacklist.html - - - /reference/overlap_heatmap.html - - - /reference/overlap_percent.html - - - /reference/overlap_stat_plot.html - - - /reference/overlap_upset_plot.html - - - /reference/peak_info.html - - - /reference/plot_ChIPseeker_annotation.html - - - /reference/plot_chromHMM.html - - - /reference/plot_corr.html - - - /reference/plot_enrichment.html - - - /reference/plot_precision_recall.html - - - /reference/precision_recall.html - - - /reference/precision_recall_matrix.html - - - /reference/predict_precision_recall.html - - - /reference/predict_values.html - - - /reference/prepare_blacklist.html - - - /reference/prepare_genome_builds.html - - - /reference/prepare_peaklist.html - - - /reference/prepare_reference.html - - - /reference/read_bowtie.html - - - /reference/read_peaks.html - - - /reference/rebin_peaks.html - - - /reference/remove_nonstandard_chrom.html - - - /reference/report_command.html - - - /reference/report_header.html - - - /reference/save_output.html - - - /reference/set_min_max.html - - - /reference/stopper.html - - - /reference/tidy_peakfile.html - - - /reference/translate_genome.html - - - /reference/tss_plot.html - - - /reference/width_boxplot.html - - - /reference/write_example_peaks.html - + +/404.html +/articles/EpiCompare.html +/articles/docker.html +/articles/example_report.html +/articles/index.html +/authors.html +/index.html +/news/index.html +/reference/CnR_H3K27ac.html +/reference/CnR_H3K27ac_picard.html +/reference/CnT_H3K27ac.html +/reference/CnT_H3K27ac_picard.html +/reference/EpiCompare.html +/reference/as_interactive.html +/reference/bpplapply.html +/reference/checkCache.html +/reference/check_cell_lines.html +/reference/check_genome_build.html +/reference/check_grlist_cols.html +/reference/check_list_names.html +/reference/check_workers.html +/reference/clean_granges.html +/reference/compute_consensus_peaks.html +/reference/compute_corr.html +/reference/download_button.html +/reference/encode_H3K27ac.html +/reference/fig_length.html +/reference/fragment_info.html +/reference/gather_files.html +/reference/gather_files_names.html +/reference/get_bpparam.html +/reference/get_chromHMM_annotation.html +/reference/group_files.html +/reference/hg19_blacklist.html +/reference/hg38_blacklist.html +/reference/index.html +/reference/is_granges.html +/reference/liftover_grlist.html +/reference/message_parallel.html +/reference/messager.html +/reference/mm10_blacklist.html +/reference/mm9_blacklist.html +/reference/overlap_heatmap.html +/reference/overlap_percent.html +/reference/overlap_stat_plot.html +/reference/overlap_upset_plot.html +/reference/peak_info.html +/reference/plot_ChIPseeker_annotation.html +/reference/plot_chromHMM.html +/reference/plot_corr.html +/reference/plot_enrichment.html +/reference/plot_precision_recall.html +/reference/precision_recall.html +/reference/precision_recall_matrix.html +/reference/predict_precision_recall.html +/reference/predict_values.html +/reference/prepare_blacklist.html +/reference/prepare_genome_builds.html +/reference/prepare_peaklist.html +/reference/prepare_reference.html +/reference/read_bowtie.html +/reference/read_peaks.html +/reference/rebin_peaks.html +/reference/remove_nonstandard_chrom.html +/reference/report_command.html +/reference/report_header.html +/reference/save_output.html +/reference/set_min_max.html +/reference/stopper.html +/reference/tidy_chromosomes.html +/reference/tidy_peakfile.html +/reference/translate_genome.html +/reference/tss_plot.html +/reference/width_boxplot.html +/reference/write_example_peaks.html +