add drop=FALSE to all FraserDataSet subsetting in countRNA

gagneurlab · Feb 5, 2024 · 4a15970 · 4a15970
1 parent e650af9
commit 4a15970
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -232,7 +232,7 @@ setReplaceMethod("nonSplicedReads", "FraserDataSet", function(object, value){
 #' @param j A integer vector to subset the columns/samples
 #' @param by a character (j or ss) defining if we subset by
 #'             junctions or splice sites
-#' @param drop Currently not used 
+#' @param dropBool Currently not used 
 #' @return A subsetted \code{FraserDataSet} object
 #' @examples
 #'     fds <- createTestFraserDataSet()
@@ -289,14 +289,14 @@ subset.FRASER <- function(x, i, j, by=c("j", "ss"), drop = FALSE){
         idxNSR <- rowData(x, type="ss")[['spliceSiteID']] %in% ssIdx
 
         # subset it
-        nsrObj <- nsrObj[idxNSR,j]
+        nsrObj <- nsrObj[idxNSR,j,drop=FALSE]
     }
 
     # subset the inheritate SE object
     if(length(x) == 0){
         i <- NULL
     }
-    subX <- as(as(x, "RangedSummarizedExperiment")[i,j], "FraserDataSet")
+    subX <- as(as(x, "RangedSummarizedExperiment")[i,j,drop=FALSE], "FraserDataSet")
 
     # create new FraserDataSet object
     newx <- new("FraserDataSet",

diff --git 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]),
-                    pairedend=pairedEnd(fds[,sampleID]),
+                    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])[[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])[[1]]
+    isPairedEnd <- pairedEnd(fds[,samples(fds) == sampleID,drop=FALSE])[[1]]
     doAutosort <- isPairedEnd
 
     # check cache if available