Port tidyChromosomes from BRGenomics package

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: EpiCompare
 Title: Comparison, Benchmarking & QC of Epigenomic Datasets
-Version: 1.7.5
+Version: 1.9.5
 Authors@R: c(
     person(given = "Sera", family = "Choi", 
         email = "[email protected]", 
@@ -24,7 +24,11 @@ Authors@R: c(
         comment = c(ORCID = "0000-0002-6807-3180")),
     person(given="Thomas", family="Roberts",
         email = "[email protected]",
-        role = "cre")
+        role = "ctb"),
+    person(given="Hiranyamaya", family="Dash", 
+        email = "[email protected]",
+        role = "cre",
+        comment = c(ORCID = "0009-0005-5514-505X"))
   )
 Description: EpiCompare is used to compare and analyse epigenetic datasets 
   for quality control and benchmarking purposes. 
@@ -44,7 +48,6 @@ Depends:
     R (>= 4.2.0)
 Imports:
     AnnotationHub,
-    BRGenomics,
     ChIPseeker,
     data.table,
     genomation,
@@ -98,4 +101,4 @@ biocViews: Epigenetics, Genetics, QualityControl, ChIPSeq,
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: FALSE
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

NAMESPACE

@@ -25,6 +25,7 @@ export(predict_precision_recall)
 export(rebin_peaks)
 export(report_command)
 export(report_header)
+export(tidy_chromosomes)
 export(tidy_peakfile)
 export(translate_genome)
 export(tss_plot)
@@ -33,7 +34,6 @@ export(write_example_peaks)
 import(GenomicRanges)
 import(ggplot2)
 importFrom(AnnotationHub,AnnotationHub)
-importFrom(BRGenomics,tidyChromosomes)
 importFrom(BiocGenerics,"%in%")
 importFrom(BiocGenerics,`%in%`)
 importFrom(ChIPseeker,annotatePeak)
@@ -42,13 +42,17 @@ importFrom(ChIPseeker,getPromoters)
 importFrom(ChIPseeker,getTagMatrix)
 importFrom(ChIPseeker,plotAvgProf)
 importFrom(ChIPseeker,readPeakFile)
+importFrom(GenomeInfoDb,"genome<-")
 importFrom(GenomeInfoDb,Seqinfo)
+importFrom(GenomeInfoDb,genome)
+importFrom(GenomeInfoDb,keepSeqlevels)
 importFrom(GenomeInfoDb,mapGenomeBuilds)
 importFrom(GenomeInfoDb,seqlevels)
 importFrom(GenomeInfoDb,seqlevelsInUse)
 importFrom(GenomeInfoDb,seqlevelsStyle)
 importFrom(GenomeInfoDb,seqnames)
 importFrom(GenomeInfoDb,sortSeqlevels)
+importFrom(GenomeInfoDb,standardChromosomes)
 importFrom(GenomicRanges,GRanges)
 importFrom(GenomicRanges,GRangesList)
 importFrom(GenomicRanges,binnedAverage)

NEWS.md

@@ -1,3 +1,14 @@
+## 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
 
 ### New features

R/peak_info.R

@@ -11,7 +11,6 @@
 #' @return A summary table of peak information
 #'
 #' @importMethodsFrom IRanges subsetByOverlaps
-#' @importFrom BRGenomics tidyChromosomes
 #' @export
 #'
 #' @examples
@@ -46,7 +45,7 @@ peak_info <- function(peaklist, blacklist){
 
   ### Obtain Non-standard Chromosome Percentage ###
   tidy_percent <- mapply(peaklist, FUN=function(file){
-    peak_tidy <- BRGenomics::tidyChromosomes(file, keep.X = TRUE, keep.Y = TRUE)
+    peak_tidy <- tidy_chromosomes(file, keep.X = TRUE, keep.Y = TRUE)
     removedN <- length(file) - length(peak_tidy)
     percentage <- signif(removedN/length(file)*100, 3)
   })

R/tidy_chromosomes.R

@@ -0,0 +1,78 @@
+#' Remove odd chromosomes from GRanges objects
+#'
+#' This convenience function removes non-standard, mitochondrial, and/or sex
+#' chromosomes from any GRanges object.
+#' 
+#' This function is adapted from \code{tidyChromosomes} in the
+#' \code{BRGenomics} package licensed under the Artistic License 2.0.
+#' Original author: Mike DeBerardine <https://github.com/mdeber>
+#'
+#' @param gr Any GRanges object, or any another object with associated
+#'   \code{seqinfo} (or a \code{Seqinfo} object itself). The object should
+#'   typically have a standard genome associated with it, e.g. \code{genome(gr)
+#'   <- "hg38"}. \code{gr} can also be a list of such GRanges objects.
+#' @param 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.
+#' @param genome An optional string that, if supplied, will be used to set the
+#'   genome of \code{gr}.
+#'
+#' @return A GRanges object in which both ranges and \code{seqinfo} associated
+#'   with trimmed chromosomes have been removed.
+#'
+#' @details Standard chromosomes are defined using the
+#'   \code{\link[GenomeInfoDb:seqlevels-wrappers]{standardChromosomes}} function
+#'   from the \code{GenomeInfoDb} package.
+#'
+#' @author Mike DeBerardine
+#' @seealso \code{\link[GenomeInfoDb:seqlevels-wrappers]{
+#'   GenomeInfoDb::standardChromosomes}}
+#'
+#' @export
+#' @importFrom GenomeInfoDb standardChromosomes seqlevels keepSeqlevels
+#'   sortSeqlevels genome genome<-
+#' @importFrom methods is
+#' @examples
+#' # make a GRanges
+#' chrom <- c("chr2", "chr3", "chrX", "chrY", "chrM", "junk")
+#' gr <- GRanges(seqnames = chrom,
+#'               ranges = IRanges(start = 2*(1:6), end = 3*(1:6)),
+#'               strand = "+",
+#'               seqinfo = Seqinfo(chrom))
+#' genome(gr) <- "hg38"
+#'
+#' gr
+#'
+#' tidy_chromosomes(gr)
+#'
+#' tidy_chromosomes(gr, keep.M = TRUE)
+#'
+#' tidy_chromosomes(gr, keep.M = TRUE, keep.Y = FALSE)
+#'
+#' tidy_chromosomes(gr, keep.nonstandard = TRUE)
+#' 
+#' @keywords internal
+tidy_chromosomes <- function(gr, keep.X = TRUE, keep.Y = TRUE, keep.M = FALSE,
+                            keep.nonstandard = FALSE, genome = NULL) {
+
+    if (is.list(gr) || is(gr, "GRangesList"))
+        return(lapply(gr, tidy_chromosomes, keep.X, keep.Y, keep.M,
+                      keep.nonstandard, genome))
+
+    if (!is.null(genome))
+        genome(gr) <- genome
+
+    chrom <- standardChromosomes(gr)
+
+    if (keep.nonstandard) chrom <- seqlevels(gr)
+    if (!keep.X)  chrom <- chrom[ chrom != "chrX" ]
+    if (!keep.Y)  chrom <- chrom[ chrom != "chrY" ]
+    if (!keep.M)  chrom <- chrom[ (chrom != "chrM") & (chrom != "chrMT") ]
+
+    if (is(gr, "Seqinfo")) {
+        gr <- keepSeqlevels(gr, chrom)
+    } else {
+        gr <- keepSeqlevels(gr, chrom, pruning.mode = "tidy")
+    }
+    sortSeqlevels(gr)
+}

R/tidy_peakfile.R

@@ -14,9 +14,8 @@
 #' @return list of GRanges object
 #' @export
 #'
-#' @importFrom BRGenomics tidyChromosomes
 #' @importMethodsFrom IRanges subsetByOverlaps
-
+#'
 #' @examples
 #' ### Load Data ###
 #' data("encode_H3K27ac") # example peakfile GRanges object
@@ -36,9 +35,7 @@ tidy_peakfile <- function(peaklist, blacklist){
   ### standardise peakfiles ###
   peaklist_tidy <- mapply(peaklist, FUN = function(file){
     # remove non-standard chromosomes
-    sample <- BRGenomics::tidyChromosomes(file,
-                                          keep.X = TRUE,
-                                          keep.Y = TRUE)
+    sample <- tidy_chromosomes(file, keep.X = TRUE, keep.Y = TRUE)
     # remove blacklisted regions
     IRanges::subsetByOverlaps(sample,
                               blacklist,