Fix BioC 3.23 compatibility: pwalign, C++14, jaspar_db docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: chromVAR
 Type: Package
 Title: Chromatin Variation Across Regions
-Version: 1.5.0
+Version: 1.35.1
 Authors@R: c(
     person("Alicia", "Schep", email = "aschep@gmail.com", role = c("aut","cre")),
     person("Jason", "Buenrostro", role = "ctb"),
@@ -15,13 +15,14 @@ Description: Determine variation in chromatin accessibility across sets of
 License: MIT + file LICENSE
 Imports:
     IRanges,
-    GenomeInfoDb,
+    Seqinfo,
     GenomicRanges,
     ggplot2,
     nabor,
     BiocParallel,
     BiocGenerics,
     Biostrings,
+    pwalign,
     TFBSTools,
     Rsamtools,
     S4Vectors,
@@ -54,6 +55,6 @@ Suggests:
 biocViews: SingleCell, Sequencing, GeneRegulation, ImmunoOncology
 LazyData: TRUE
 LinkingTo: Rcpp, RcppArmadillo
-SystemRequirements: C++11
+SystemRequirements: C++14
 VignetteBuilder: knitr
-RoxygenNote: 6.0.1
+RoxygenNote: 7.3.2

NAMESPACE

@@ -70,14 +70,10 @@ importClassesFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(BSgenome,getBSgenome)
 importFrom(BiocGenerics,relist)
 importFrom(BiocParallel,bplapply)
-importFrom(Biostrings,nucleotideSubstitutionMatrix)
-importFrom(Biostrings,stringDist)
+importFrom(pwalign,nucleotideSubstitutionMatrix)
+importFrom(pwalign,stringDist)
 importFrom(DT,datatable)
 importFrom(DT,formatSignif)
-importFrom(GenomeInfoDb,"seqlevels<-")
-importFrom(GenomeInfoDb,seqlevels)
-importFrom(GenomeInfoDb,seqnames)
-importFrom(GenomeInfoDb,sortSeqlevels)
 importFrom(IRanges,IRanges)
 importFrom(IRanges,PartitioningByEnd)
 importFrom(IRanges,overlapsAny)
@@ -91,6 +87,10 @@ importFrom(S4Vectors,elementNROWS)
 importFrom(S4Vectors,isSorted)
 importFrom(S4Vectors,queryHits)
 importFrom(S4Vectors,subjectHits)
+importFrom(Seqinfo,"seqlevels<-")
+importFrom(Seqinfo,seqlevels)
+importFrom(Seqinfo,seqnames)
+importFrom(Seqinfo,sortSeqlevels)
 importFrom(TFBSTools,PWMatrix)
 importFrom(TFBSTools,PWMatrixList)
 importFrom(TFBSTools,bg)

R/background_peaks.R

@@ -22,7 +22,7 @@ setGeneric("addGCBias", function(object, ...) standardGeneric("addGCBias"))
 #' @export
 setMethod(addGCBias, c(object = "RangedSummarizedExperiment"), 
           function(object, 
-                   genome = GenomeInfoDb::genome(object)) {
+                   genome = Seqinfo::genome(object)) {
             genome <- validate_genome_input(genome)
             peaks <- rowRanges(object)
             seqs <- getSeq(genome, peaks)
@@ -38,7 +38,7 @@ setMethod(addGCBias, c(object = "RangedSummarizedExperiment"),
 #' @export
 setMethod(addGCBias, c(object = "SummarizedExperiment"), 
           function(object, peaks, 
-                   genome = GenomeInfoDb::genome(peaks)) {
+                   genome = Seqinfo::genome(peaks)) {
             genome <- validate_genome_input(genome)
             seqs <- getSeq(genome, peaks)
             nucfreqs <- letterFrequency(seqs, c("A", "C", "G", "T"))

R/chromVAR.R

@@ -21,7 +21,7 @@
 #' txtProgressBar
 #' @importFrom Rcpp sourceCpp
 #' @importFrom S4Vectors queryHits subjectHits DataFrame elementNROWS isSorted
-#' @importFrom GenomeInfoDb seqlevels seqlevels<- sortSeqlevels seqnames
+#' @importFrom Seqinfo seqlevels seqlevels<- sortSeqlevels seqnames
 #' @importFrom Rsamtools ScanBamParam scanBamFlag scanBam countBam
 #' @importFrom IRanges IRanges overlapsAny
 #' @importFrom BiocParallel bplapply

R/kmers.R

@@ -56,7 +56,7 @@ deviationsCovariability <- function(object) {
   return(normed_covs)
 }
 
-#' @importFrom Biostrings nucleotideSubstitutionMatrix stringDist
+#' @importFrom pwalign nucleotideSubstitutionMatrix stringDist
 get_kmer_dist <- function(kmers) {
   stopifnot(all_equal(nchar(kmers)))
   out <- as.matrix(stringDist(kmers, 

R/match_kmers.R

@@ -153,7 +153,7 @@ setMethod("matchKmers", signature(k = "character", subject = "DNAString"),
 setMethod("matchKmers", signature(k = "character", subject = "GenomicRanges"),
           function(k,
                    subject, 
-                   genome = GenomeInfoDb::genome(subject),
+                   genome = Seqinfo::genome(subject),
                    out = c("matches", "positions")) {
             out <- match.arg(out)
             GenomicRanges::strand(subject) <- "+"

R/motifs.R

@@ -1,28 +1,33 @@
 #' getJasparMotifs
 #'
 #' Function to get motifs from JASPAR database
-#' @param species Which species?  use eithe jaspar code or latin name. 
+#' @param species Which species?  use eithe jaspar code or latin name.
 #' default is 'Homo sapiens'
 #' @param collection Which collection to use?  default is 'CORE'
-#' @param ... additional arguments to opts for 
+#' @param jaspar_db Which JASPAR database? default is `JASPAR2016::JASPAR2016`
+#' @param ... additional arguments to opts for
 #' \code{\link[TFBSTools]{getMatrixSet}}
 #' @details Simply a wrapper function for \code{\link[TFBSTools]{getMatrixSet}}
 #'  that calls JASPAR2016 database using \code{\link[JASPAR2016]{JASPAR2016}}
 #' @return \code{\link[TFBSTools]{PFMatrixList}}
 #' @export
-#' @examples 
-#' 
+#' @examples
+#'
 #' motifs <- getJasparMotifs()
-#' 
-#' 
-getJasparMotifs <- function(species = "Homo sapiens", 
-                              collection = "CORE", ...) {
+#'
+#' # use the JASPAR2020 database
+#' motifs <- getJasparMotifs(jaspar_db = JASPAR2020::JASPAR2020)
+#'
+getJasparMotifs <- function(species = "Homo sapiens",
+                            collection = "CORE",
+                            jaspar_db = JASPAR2016::JASPAR2016,
+                            ...) {
   opts <- list()
   opts["species"] <- species
   opts["collection"] <- collection
   opts <- c(opts, list(...))
-  out <- TFBSTools::getMatrixSet(JASPAR2016::JASPAR2016, opts)
-  if (!isTRUE(all.equal(TFBSTools::name(out), names(out)))) 
+  out <- TFBSTools::getMatrixSet(jaspar_db, opts)
+  if (!isTRUE(all.equal(TFBSTools::name(out), names(out))))
     names(out) <- paste(names(out), TFBSTools::name(out), sep = "_")
   return(out)
 }

data-raw/example_counts.R

@@ -17,7 +17,7 @@ cleanup_peaks <- function(peaks){
   non_mito_peaks = which(!blacklisted)
   peaks <- peaks[non_mito_peaks]
 
-  seqlengths(peaks) <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)[GenomeInfoDb::seqlevels(peaks)]
+  seqlengths(peaks) <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)[Seqinfo::seqlevels(peaks)]
   within_boundaries = which(GenomicRanges::trim(peaks) == peaks)
   peaks <- peaks[within_boundaries]
   return(peaks)