Merge remote-tracking branch 'upstream/master'

sartorlab · Jul 9, 2019 · 6b19c7d · 6b19c7d
2 parents d261e4a + 46e7a79
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: chipenrich
 Type: Package
 Title: Gene Set Enrichment For ChIP-seq Peak Data
-Version: 2.5.0
-Date: 2018-04-30
+Version: 2.9.1
+Date: 2019-06-08
 Authors@R: c(
 	person(c("Ryan","P."),"Welch",role = c("aut","cph"),email = "welchr@umich.edu"),
 	person("Chee","Lee",role = c("aut"),email = "cheelee@umich.edu"),
@@ -14,7 +14,7 @@ Description: ChIP-Enrich performs gene set enrichment testing
     using peaks called from a ChIP-seq experiment. The method empirically
     corrects for confounding factors such as the length of genes,
     and the mappability of the sequence surrounding genes.
-biocViews: ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, Regression
+biocViews: ImmunoOncology, ChIPSeq, Epigenetics, FunctionalGenomics, GeneSetEnrichment, HistoneModification, Regression
 License: GPL-3
 Imports:
 	AnnotationDbi,
@@ -38,7 +38,7 @@ Imports:
 	plyr,
 	rms,
 	rtracklayer,
-	S4Vectors,
+	S4Vectors (>= 0.23.10),
 	stats,
 	stringr,
 	utils

diff --git a/NAMESPACE b/NAMESPACE
@@ -40,6 +40,7 @@ importFrom(BiocGenerics,unlist)
 importFrom(GenomeInfoDb,seqinfo)
 importFrom(IRanges,IRanges)
 importFrom(S4Vectors,queryHits)
+importFrom(S4Vectors,splitAsList)
 importFrom(S4Vectors,subjectHits)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,pdf)

diff --git a/R/chipenrich_package_doc.R b/R/chipenrich_package_doc.R
@@ -26,7 +26,7 @@
 #' @importFrom plyr rbind.fill
 #' @import rms
 #' @import rtracklayer
-#' @importFrom S4Vectors queryHits subjectHits
+#' @importFrom S4Vectors queryHits subjectHits splitAsList
 #' @importFrom stats as.formula binom.test coef complete.cases fisher.test fitted na.omit p.adjust pchisq predict qpois quantile resid
 #' @importFrom stringr str_match str_sub
 #' @importFrom utils data read.table tail write.table

diff --git a/R/randomize.R b/R/randomize.R
@@ -17,7 +17,7 @@ randomize_ldef_bylocation = function(ldef, resolution=50) {
 			# Create groups within the chromosome
 			group = floor( (seq_along(gr) + (resolution - 1)) / resolution )
 			# Split by the group
-			grl = IRanges::splitAsList(gr, group)
+			grl = S4Vectors::splitAsList(gr, group)
 			# Rearrange mcols within each group
 			re_grl = S4Vectors::endoapply(grl, function(grg){
 				GenomicRanges::mcols(grg) = GenomicRanges::mcols(grg)[sample(seq_along(grg), length(grg)),]

diff --git a/inst/doc/chipenrich-vignette.R b/inst/doc/chipenrich-vignette.R