Merge pull request #3 from Novartis/devel

Merge pull request #2 from Novartis/main
Novartis · Feb 17, 2025 · ba80246 · ba80246
2 parents 83a917d + f5aaf9d
commit ba80246
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -2,3 +2,6 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^data-raw$
+.github$
+combpeaksr.Rproj
+LICENSE.txt
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -19,20 +19,20 @@ jobs:
       matrix:
         config:
           - { os: windows-latest, bioc: 'devel', deploy: 'no'}
-          - { os: macOS-12, bioc: 'devel', deploy: 'yes'}
+          - { os: macOS-latest, bioc: 'devel', deploy: 'yes'}
           # - { os: ubuntu-latest, r: 'devel', image: 'bioconductor/bioconductor_docker:devel', deploy: 'no'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       CRAN: ${{ matrix.config.cran }}
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      cache-version: v2
+      cache-version: v3
 
     steps:
-      - name: checkout branch
+      - name: Checkout code
         uses: actions/checkout@v3
-
+      
       - name: Set up R and install BiocManager
         uses: grimbough/bioc-actions/setup-bioc@v1
         if: matrix.config.image == null
@@ -55,7 +55,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows' && matrix.config.image == null
-        uses: actions/cache@v1
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ env.cache-version }}-${{ runner.os }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }}
@@ -102,11 +102,24 @@ jobs:
 
       - name: Upload install log if the build/install/check step fails
         if: always() && (steps.build-install-check.outcome == 'failure')
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: install-log
           path: |
             ${{ steps.build-install-check.outputs.install-log }}
+            
+      - name: Install dependencies
+        run: |
+          install.packages("rlang")
+          install.packages("testthat")
+        shell: Rscript {0}
+
+      - name: Run tests and capture output
+        run: |
+          sink(file = "tests/testthat.Rout")
+          testthat::test_dir("tests/testthat")
+          sink()
+        shell: Rscript {0}
 
       - name: Show testthat output (windows)
         if: always() && runner.os == 'Windows'
@@ -133,17 +146,19 @@ jobs:
           arguments: '--no-check-bioc-views --no-check-bioc-help'
           error-on: 'error'
 
-      - name: Test coverage
-        if: matrix.config.os == 'macOS-12' && matrix.config.bioc == 'devel'
-        run: |
-          install.packages("covr")
-          covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")
-        shell: Rscript {0}
+      #- name: Test coverage
+      #  if: matrix.config.os == 'macOS-latest' && matrix.config.bioc == 'devel'
+      #  run: |
+      #    install.packages("covr")
+      #    covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")
+      #  shell: Rscript {0}
 
       - name: Deploy
         if: github.event_name == 'push' && github.ref == 'refs/heads/devel' && matrix.config.deploy == 'yes'
         run: |
           R CMD INSTALL .
           Rscript -e "remotes::install_dev('pkgdown'); pkgdown::deploy_to_branch(new_process = FALSE)"
+    
+
 
 
diff --git a/.gitignore b/.gitignore
@@ -2,4 +2,5 @@
 .Rhistory
 .RData
 .Ruserdata
+.github
 inst/doc
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: peakCombiner
 Title: The R package to curate and merge enriched genomic regions into consensus peak sets
-Version: 0.99.4
+Version: 0.99.1
 Description: peakCombiner, a fully R based, user-friendly, transparent, and customizable tool that allows even novice R users to create a high-quality consensus peak list. The modularity of its functions allows an easy way to optimize input and output data. A broad range of accepted input data formats can be used to create a consensus peak set that can be exported to a file or used as the starting point for most downstream peak analyses. 
 Authors@R: c(person("Markus", "Muckenhuber",
                 email = "markusmuckenhuber@gmx.at", 
@@ -13,8 +13,10 @@ Authors@R: c(person("Markus", "Muckenhuber",
              person("Michael", "Stadler",
                 email = "",
                 role = c("aut"),
-                comment = c(ORCID = "0000-0002-2269-4934")))
-Depends: R (>= 4.2)
+                comment = c(ORCID = "0000-0002-2269-4934")),
+             person("Novartis Biomedical Research", 
+                role = c("cph")))
+Depends: R (>= 4.3.0)
 License: MIT + file LICENSE
 LazyData: FALSE
 biocViews:
@@ -23,33 +25,38 @@ biocViews:
     ChipOnChip
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Suggests: 
     testthat (>= 3.0.0),
+    tidyverse,
     rmarkdown,
     styler,
     cli,
     lintr,
     rtracklayer,
     knitr,
     devtools,
-    qpdf,
+    ggplot2,
     BiocStyle,
-    ggplot2
-DEPENDS:
-        dplyr (>= 1.1.2),
-        GenomicRanges
+    usethis,
+    utils
 Imports: 
-    stringr,
     tidyr,
-    purrr (>= 1.0.1),
+    dplyr (>= 1.1.2),
+    IRanges,
+    GenomicRanges,
+    tidyselect,
+    purrr,
     readr (>= 2.1.2),
     tibble (>= 3.2.1),
-    stats,
-    IRanges,
     rlang,
-    here
+    stringr,
+    here,
+    stats, 
+    qpdf
 URL:
-BugReports:
+    https://github.com/novartis/peakCombiner/, 
+    https://bioconductor.org/packages/peakCombiner
+BugReports: https://github.com/novartis/peakCombiner/issues
 Config/testthat/edition: 3
 VignetteBuilder: knitr
diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
 YEAR: 2023
-COPYRIGHT HOLDER: peakCombiner authors
+COPYRIGHT HOLDER: Novartis Biomedical Research
diff --git a/NAMESPACE b/NAMESPACE
@@ -4,3 +4,7 @@ export(center_expand_regions)
 export(combine_regions)
 export(filter_regions)
 export(prepare_input_regions)
+import(here)
+import(stringr)
+import(tidyr)
+importFrom(rlang,.data)
diff --git a/R/center_expand_regions.R b/R/center_expand_regions.R
@@ -57,13 +57,13 @@
 #'                      named `chrom`, `start`, `end`, `name`,
 #'                      `score`, `strand`, `center`, `sample_name`. Additional
 #'                      columns will be maintained.
-#' @param center_by   Allowed values are 'center_column' (default) or 
+#' @param center_by   Allowed values are 'center_column' (default) or
 #'                    'midpoint'.
 #' * 'center_column' uses the value stored in the column `center` to center.
-#' * 'midpoint' replaces the value stored in the column `center` with the 
-#'    mathematical mean of each genomic region (e.g., round(end - start / 2)), 
+#' * 'midpoint' replaces the value stored in the column `center` with the
+#'    mathematical mean of each genomic region (e.g., round(end - start / 2)),
 #'    which is then used.
-#'    
+#'
 #' @param expand_by   Allowed values a numeric vector of length 1 or 2,
 #'                      or 'NULL' (default).
 #' * The value from the numeric vector of length 1
@@ -94,17 +94,17 @@
 #'
 #' @export
 #'
+#' @importFrom rlang .data
+#' @import tidyr
+#' @import here
+#'
 #' @examples
 #' # Load in and prepare a an accepted tibble
-#' sample_sheet <- readr::read_tsv(
-#'   paste0(infolder, "/lists/synthetic_sample_sheet.tsv"),
-#'   show_col_types = FALSE
-#' )
-#' sample_sheet
+#' utils::data(syn_data_bed)
 #'
 #' # Prepare input data
 #' data_prepared <- prepare_input_regions(
-#'   data = sample_sheet,
+#'   data = syn_data_bed,
 #'   show_messages = TRUE
 #' )
 #' # Run center and expand
@@ -132,7 +132,6 @@ center_expand_regions <- function(data,
                                   center_by = "center_column",
                                   expand_by = NULL,
                                   show_messages = TRUE) {
-
   ### -----------------------------------------------------------------------###
   ### Show or hide messages
   ### -----------------------------------------------------------------------###
@@ -228,12 +227,12 @@ center_expand_regions <- function(data,
   ### -----------------------------------------------------------------------###
   ### Center and expand
   ### -----------------------------------------------------------------------###
-  
+
   cli::cli_inform(c(
     ">" = "Genomic regions will be centered and expanded.",
     " " = " "
   ))
-  
+
   if (center_by == "center_column") {
     cli::cli_inform(c(
       ">" = "Starting with expanding genomic regions from the column {.field

diff --git a/R/center_expand_regions_helper.R b/R/center_expand_regions_helper.R
@@ -10,14 +10,9 @@
 #'
 #' @return A vector of length 1 to define region expansion.
 #'
-#' @examples
-#' expansion_value <- define_expansion(
-#'   data = data,
-#'   expand_by = expand_by
-#' )
+
 define_expansion <- function(data = data,
                              expand_by = expand_by) {
-
   ### -----------------------------------------------------------------------###
   ### Pre-Check up
   ### -----------------------------------------------------------------------###

diff --git a/R/check_data_structure.R b/R/check_data_structure.R
@@ -1,7 +1,7 @@
 #' Control structure of peakCombiner data structure
 #'
 #' @description
-#' This is a general helper function for the package [peakCombiner]. Aim of this
+#' This is a general helper function for the package \pkg{peakCombiner}. Aim of this
 #' function is to check a data frame for the correct column names and classes of
 #' each column to ensure to be an accepte inpuut for functions:
 #' [peakCombiner::center_expand_regions()], [peakCombiner::filter_regions()] and
@@ -18,7 +18,6 @@
 #' [peakCombiner::combine_regions()].
 #'
 check_data_structure <- function(data) {
-
   ### -----------------------------------------------------------------------###
   ### Define variables
   ### -----------------------------------------------------------------------###

diff --git a/R/combine_regions.R b/R/combine_regions.R
@@ -94,17 +94,17 @@
 #'
 #' @export
 #'
-#' @examples
+#' @importFrom rlang .data
+#' @import stringr
+#' @import tidyr
+#' @import here
 #'
-#' # Load in and prepare input data
-#' sample_sheet <- readr::read_tsv(
-#'   paste0(infolder, "/lists/synthetic_sample_sheet.tsv"),
-#'   show_col_types = FALSE
-#' )
-#' sample_sheet
+#' @examples
+#' # Load in and prepare a an accepted tibble
+#' utils::data(syn_data_bed)
 #'
 #' data_prepared <- prepare_input_regions(
-#'   data = sample_sheet,
+#'   data = syn_data_bed,
 #'   show_messages = FALSE
 #' )
 #'
@@ -124,11 +124,12 @@ combine_regions <- function(data,
                             annotate_with_input_names = FALSE,
                             combined_sample_name = NULL,
                             show_messages = TRUE) {
-
   ### -----------------------------------------------------------------------###
   ### Correct parameters & load needed variables
   ### -----------------------------------------------------------------------###
-
+  ##
+  set.seed(1234)
+  ##
   ### -----------------------------------------------------------------------###
   ### Show or hide messages
   ### -----------------------------------------------------------------------###
@@ -204,7 +205,7 @@ combine_regions <- function(data,
 
 
   data_combined_with_summit <- data_combined_with_summit |>
-    dplyr::relocate(.data$strand, .after = .data$score) |>
+    dplyr::relocate("strand", .after = "score") |>
     dplyr::mutate(strand = ifelse(.data$strand == "*", ".", .data$strand)) |>
     dplyr::ungroup()