Merge pull request #2 from Novartis/main

.Rbuildignore

@@ -2,3 +2,6 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^data-raw$
+.github$
+combpeaksr.Rproj
+LICENSE.txt

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

@@ -107,6 +107,21 @@ jobs:
           name: install-log
           path: |
             ${{ steps.build-install-check.outputs.install-log }}
+
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: Rscript -e 'install.packages("testthat")'
+
+      - name: Run tests and capture output
+        run: |
+          sink("tests/testthat/testthat.Rout")
+          testthat::test_dir("tests/testthat")
+          sink()
 
       - name: Show testthat output (windows)
         if: always() && runner.os == 'Windows'
@@ -133,17 +148,19 @@ 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 = "${{secrets.CODECOV_TOKEN}}")
-        shell: Rscript {0}
+      #- name: Test coverage
+      #  if: matrix.config.os == 'macOS-12' && matrix.config.bioc == 'devel'
+      #  run: |
+      #    install.packages("covr")
+      #    covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")
+      #  shell: Rscript {0}
 
       - name: Deploy
         if: github.event_name == 'push' && github.ref == 'refs/heads/devel' && matrix.config.deploy == 'yes'
         run: |
           R CMD INSTALL .
           Rscript -e "remotes::install_dev('pkgdown'); pkgdown::deploy_to_branch(new_process = FALSE)"
+
+
 
 

.gitignore

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

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: 0.99.5
 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 = "[email protected]", 
@@ -14,9 +14,9 @@ Authors@R: c(person("Markus", "Muckenhuber",
                 email = "",
                 role = c("aut"),
                 comment = c(ORCID = "0000-0002-2269-4934")))
-Depends: R (>= 4.2)
+Depends: R (>= 4.3.0)
 License: MIT + file LICENSE
-LazyData: FALSE
+LazyData: TRUE
 biocViews:
     WorkflowStep,
     Preprocessing,
@@ -26,6 +26,7 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Suggests: 
     testthat (>= 3.0.0),
+    tidyverse,
     rmarkdown,
     styler,
     cli,
@@ -34,22 +35,32 @@ Suggests:
     knitr,
     devtools,
     qpdf,
-    BiocStyle,
-    ggplot2
+    ggplot2,
+    BiocStyle
 DEPENDS:
         dplyr (>= 1.1.2),
-        GenomicRanges
+        GenomicRanges,
+        IRanges,
+        tidyr,
+        tidyselect,
+        usethis,
+        utils,
+        stats
 Imports: 
-    stringr,
-    tidyr,
-    purrr (>= 1.0.1),
-    readr (>= 2.1.2),
-    tibble (>= 3.2.1),
-    stats,
-    IRanges,
-    rlang,
-    here
+        tidyr,
+        dplyr,
+        IRanges,
+        GenomicRanges,
+        tidyselect,
+        purrr,
+        readr (>= 2.1.2),
+        tibble (>= 3.2.1),
+        rlang,
+        stringr,
+        here
 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

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)

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 +94,18 @@
 #'
 #' @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
+#' input_data <- peakCombiner::syn_data_bed
+#' input_data
 #'
 #' # Prepare input data
 #' data_prepared <- prepare_input_regions(
-#'   data = sample_sheet,
+#'   data = input_data,
 #'   show_messages = TRUE
 #' )
 #' # Run center and expand
@@ -132,7 +133,6 @@ center_expand_regions <- function(data,
                                   center_by = "center_column",
                                   expand_by = NULL,
                                   show_messages = TRUE) {
-
   ### -----------------------------------------------------------------------###
   ### Show or hide messages
   ### -----------------------------------------------------------------------###
@@ -228,12 +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

@@ -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
   ### -----------------------------------------------------------------------###

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
   ### -----------------------------------------------------------------------###

R/combine_regions.R

@@ -94,17 +94,18 @@
 #'
 #' @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
+#' input_data <- peakCombiner::syn_data_bed
+#' input_data
 #'
 #' data_prepared <- prepare_input_regions(
-#'   data = sample_sheet,
+#'   data = input_data,
 #'   show_messages = FALSE
 #' )
 #'
@@ -124,11 +125,12 @@ 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 +206,7 @@ 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()