Checked Style. And temporarily removed CodeCov

.github/workflows/R-CMD-check.yaml

@@ -133,12 +133,12 @@ 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 = "${{secrets.CODECOV_TOKEN}}")
-        shell: Rscript {0}
+      #- name: Test coverage
+      #  if: matrix.config.os == 'macOS-12' && matrix.config.bioc == 'devel'
+      #  run: |
+      #    install.packages("covr")
+      #    covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")
+      #  shell: Rscript {0}
 
       - name: Deploy
         if: github.event_name == 'push' && github.ref == 'refs/heads/devel' && matrix.config.deploy == 'yes'

.gitignore

@@ -2,4 +2,5 @@
 .Rhistory
 .RData
 .Ruserdata
+.github
 inst/doc

DESCRIPTION

@@ -34,30 +34,30 @@ Suggests:
     knitr,
     devtools,
     qpdf,
-    BiocStyle,
-    ggplot2
+    BiocStyle
 DEPENDS:
         dplyr (>= 1.1.2),
         GenomicRanges,
         tidyr,
-        dplyr,
         tidyselect,
         stringr,
         usethis,
-        utils
+        utils,
+        stats
 Imports: 
+        tidyr,
+        dplyr,
+         IRanges,
+        GenomicRanges,
+        tidyselect,
+        ggplot2,
     purrr (>= 1.0.1),
     readr (>= 2.1.2),
     tibble (>= 3.2.1),
-    stats,
-    IRanges,
     rlang,
-    GenomicRanges, 
-    tidyselect,
-    dplyr,
-    tidyr,
     here
-URL:https://github.com/novartis/peakCombiner/, 
+URL:
+    https://github.com/novartis/peakCombiner/, 
     https://bioconductor.org/packages/peakCombiner
 BugReports:https://github.com/novartis/peakCombiner/issues
 Config/testthat/edition: 3

NAMESPACE

@@ -5,5 +5,5 @@ export(combine_regions)
 export(filter_regions)
 export(prepare_input_regions)
 import(here)
-import(rlang)
 import(tidyr)
+importFrom(rlang,.data)

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
@@ -94,21 +94,21 @@
 #'
 #' @export
 #'
-#' @import rlang
+#' @importFrom rlang .data
 #' @import tidyr
 #' @import here
 #'
 #' @examples
-#' #Load in and prepare a an accepted tibble
+#' # Load in and prepare a an accepted tibble
 #' input_data <- peakCombiner::syn_data_bed
 #' input_data
 #'
-#' #Prepare input data
+#' # Prepare input data
 #' data_prepared <- prepare_input_regions(
 #'   data = input_data,
 #'   show_messages = TRUE
 #' )
-#' #Run center and expand
+#' # Run center and expand
 #' data_center_expand <- center_expand_regions(
 #'   data = data_prepared,
 #'   center_by = "center_column",
@@ -118,7 +118,7 @@
 #'
 #' data_center_expand
 #'
-#' #You can choose to use the midpoint and predefined values to expand
+#' # You can choose to use the midpoint and predefined values to expand
 #'
 #' data_center_expand <- center_expand_regions(
 #'   data = data_prepared,
@@ -133,7 +133,6 @@ center_expand_regions <- function(data,
                                   center_by = "center_column",
                                   expand_by = NULL,
                                   show_messages = TRUE) {
-
   ### -----------------------------------------------------------------------###
   ### Show or hide messages
   ### -----------------------------------------------------------------------###
@@ -159,7 +158,7 @@ center_expand_regions <- function(data,
       "i" = "Argument {.arg show_messages} is {.val {show_messages}}."
     ))
   }
-  
+
   ### -----------------------------------------------------------------------###
   ### Prepare parameters
   ### -----------------------------------------------------------------------###
@@ -229,12 +228,12 @@ 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

R/center_expand_regions_helper.R

@@ -13,7 +13,6 @@
 
 define_expansion <- function(data = data,
                              expand_by = expand_by) {
-
   ### -----------------------------------------------------------------------###
   ### Pre-Check up
   ### -----------------------------------------------------------------------###

R/check_data_structure.R

@@ -18,7 +18,6 @@
 #' [peakCombiner::combine_regions()].
 #'
 check_data_structure <- function(data) {
-
   ### -----------------------------------------------------------------------###
   ### Define variables
   ### -----------------------------------------------------------------------###

R/combine_regions.R

@@ -93,13 +93,13 @@
 #' [peakCombiner::center_expand_regions] and [peakCombiner::filter_regions].
 #'
 #' @export
-#' 
-#' @import rlang
+#'
+#' @importFrom rlang .data
 #' @import tidyr
 #' @import here
-#' 
+#'
 #' @examples
-#' #Load in and prepare a an accepted tibble
+#' # Load in and prepare a an accepted tibble
 #' input_data <- peakCombiner::syn_data_bed
 #' input_data
 #'
@@ -124,7 +124,6 @@ combine_regions <- function(data,
                             annotate_with_input_names = FALSE,
                             combined_sample_name = NULL,
                             show_messages = TRUE) {
-
   ### -----------------------------------------------------------------------###
   ### Correct parameters & load needed variables
   ### -----------------------------------------------------------------------###

R/combine_regions_helper.R

@@ -18,7 +18,6 @@
 #'
 cr_disjoin_filter <- function(data,
                               found_in_samples) {
-
   ### -----------------------------------------------------------------------###
   ### Pre-Check up
   ### -----------------------------------------------------------------------###
@@ -100,11 +99,13 @@ cr_disjoin_filter <- function(data,
     dplyr::ungroup() |>
     tidyr::unnest("revmap") |>
     dplyr::rename(chrom = "seqnames") |>
-    dplyr::left_join(data |>
-      tibble::rownames_to_column(var = "revmap") |>
-      dplyr::mutate(revmap = as.integer(.data$revmap)) |>
-      dplyr::select("revmap", "sample_name"), 
-      by = "revmap")
+    dplyr::left_join(
+      data |>
+        tibble::rownames_to_column(var = "revmap") |>
+        dplyr::mutate(revmap = as.integer(.data$revmap)) |>
+        dplyr::select("revmap", "sample_name"),
+      by = "revmap"
+    )
 
   data_disjoin_meta <- data_disjoin |>
     dplyr::left_join(
@@ -186,7 +187,6 @@ cr_disjoin_filter <- function(data,
 #'
 #'
 cr_reduce <- function(data) {
-
   ### -----------------------------------------------------------------------###
   ### Correct parameters & load needed variables
   ### -----------------------------------------------------------------------###
@@ -298,7 +298,6 @@ cr_reduce <- function(data) {
 #'
 cr_overlap_with_summits <- function(data,
                                     input) {
-
   ### -----------------------------------------------------------------------###
   ### Correct parameters & load needed variables
   ### -----------------------------------------------------------------------###
@@ -452,9 +451,9 @@ cr_overlap_with_summits <- function(data,
 #'
 #' In addition, the output data.frame columns `sample_name`, `name` and `score`
 #' will be updated.
-#' 
+#'
 #' @inheritParams combine_regions
-#' 
+#'
 #' @param input The original input file from `combine_regions` to extract center
 #' information
 #'
@@ -466,7 +465,6 @@ cr_add_summit <- function(data,
                           combined_center = "nearest",
                           annotate_with_input_names = FALSE,
                           combined_sample_name = NULL) {
-
   ### -----------------------------------------------------------------------###
   ### Correct parameters & load needed variables
   ### -----------------------------------------------------------------------###