From 49f25f91a5865bc173795ebc58d0ca9c03d4687d Mon Sep 17 00:00:00 2001 From: Drew Behrens Date: Mon, 5 Feb 2024 13:32:51 +0000 Subject: [PATCH] additional argument before drop to subset --- R/countRNAseqData.R | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/R/countRNAseqData.R b/R/countRNAseqData.R index bf015b60..b5909087 100644 --- a/R/countRNAseqData.R +++ b/R/countRNAseqData.R @@ -459,8 +459,8 @@ getSplitCountCacheFile <- function(sampleID, settings){ #' @export countSplitReads <- function(sampleID, fds, NcpuPerSample=1, genome=NULL, recount=FALSE, keepNonStandardChromosomes=TRUE, - bamfile=bamFile(fds[,sampleID,drop=FALSE]), - pairedend=pairedEnd(fds[,sampleID,drop=FALSE]), + bamfile=bamFile(fds[,sampleID,,drop=FALSE]), + pairedend=pairedEnd(fds[,sampleID,,drop=FALSE]), strandmode=strandSpecific(fds), cacheFile=getSplitCountCacheFile(sampleID, fds), scanbamparam=scanBamParam(fds), @@ -856,11 +856,11 @@ countNonSplicedReads <- function(sampleID, splitCountRanges, fds, } - bamFile <- bamFile(fds[,samples(fds) == sampleID,drop=FALSE])[[1]] + bamFile <- bamFile(fds[,samples(fds) == sampleID,,drop=FALSE])[[1]] # unstranded case: for counting only non spliced reads we # skip this information - isPairedEnd <- pairedEnd(fds[,samples(fds) == sampleID,drop=FALSE])[[1]] + isPairedEnd <- pairedEnd(fds[,samples(fds) == sampleID,,drop=FALSE])[[1]] doAutosort <- isPairedEnd # check cache if available