diff --git a/DESCRIPTION b/DESCRIPTION index b2a9346..77fbf62 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mulea Type: Package Title: Enrichment Analysis using Multiple Ontologies and False Discovery Rate -Version: 1.0.2 -Date: 2024-08-27 +Version: 1.1.0 +Date: 2024-09-24 Authors@R: c( person("Cezary", "Turek", role = "aut", comment = c(ORCID = "0000-0002-1445-5378")), diff --git a/NEWS.md b/NEWS.md index 4900b7d..f13c574 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,13 @@ -# # mulea 1.0.2 +# mulea 1.1.0 + +## Minor Improvements - Random seed argument was introduced to the ora function. +- Range in internal function `addExtraParamsToPlt()` was updated from 0 to 0.2. # mulea 1.0.1 -## BUGS +## Bug Fixes - CRAN check results indicated some OS dependent behaviour. This is now fixed. diff --git a/README.Rmd b/README.Rmd index c96ec2c..50bb213 100644 --- a/README.Rmd +++ b/README.Rmd @@ -48,7 +48,7 @@ if (!require("BiocManager", quietly = TRUE)) BiocManager::install("fgsea") ``` -To install `mulea` from [CRAN](https://cran.rstudio.com/web/packages/mulea/index.html): +To install `mulea` from [CRAN](https://cran.r-project.org/package=mulea): ```{r 'install2', eval=FALSE, message=FALSE, warning=FALSE} install.packages("mulea") diff --git a/README.md b/README.md index 7c2096f..5392f8c 100644 --- a/README.md +++ b/README.md @@ -67,7 +67,7 @@ BiocManager::install("fgsea") ``` To install `mulea` from -[CRAN](https://cran.rstudio.com/web/packages/mulea/index.html): +[CRAN](https://cran.r-project.org/package=mulea): ``` r install.packages("mulea") diff --git a/vignettes/mulea.Rmd b/vignettes/mulea.Rmd index 5b69209..4a84fd3 100644 --- a/vignettes/mulea.Rmd +++ b/vignettes/mulea.Rmd @@ -58,7 +58,7 @@ if (!require("BiocManager", quietly = TRUE)) BiocManager::install("fgsea") ``` -To install `mulea` from [CRAN](https://cran.rstudio.com/web/packages/mulea/index.html): +To install `mulea` from [CRAN](https://cran.r-project.org/package=mulea): ```{r 'install2', eval=FALSE, message=FALSE, warning=FALSE} install.packages("mulea") @@ -387,7 +387,9 @@ BH_ora_model <- ora(gmt = tf_ontology_filtered, # Background set variable background_element_names = background_set, # p-value adjustment method - p_value_adjustment_method = "BH") + p_value_adjustment_method = "BH", + # Number of processor threads to use + nthreads = 2) # Running the ORA BH_results <- run_test(BH_ora_model) @@ -399,7 +401,9 @@ Bonferroni_ora_model <- ora(gmt = tf_ontology_filtered, # Background set variable background_element_names = background_set, # p-value adjustment method - p_value_adjustment_method = "bonferroni") + p_value_adjustment_method = "bonferroni", + # Number of processor threads to use + nthreads = 2) # Running the ORA Bonferroni_results <- run_test(Bonferroni_ora_model)