Merge pull request #501 from GoekeLab/Multiplex_Fix_incompatibleCounts

Chen Ying · web-flow · commit 8ca8e90ceb6e · 2026-01-15T10:30:11.000+08:00
Fix bugs in transcriptToGeneExpression
diff --git a/R/readWrite.R b/R/readWrite.R
@@ -42,7 +42,7 @@ writeBambuOutput <- function(se, path, prefix = "", outputExtendedAnno = TRUE,
         }
         #write incompatible counts
         if(!is.null(metadata(se)$incompatibleCounts)){
-            estimates = metadata(se)$incompatibleCounts
+            estimates <- metadata(se)$incompatibleCounts
             estimatesfn <- paste(transcript_gtffn, "incompatibleCounts.mtx", sep = "")
                 Matrix::writeMM(estimates, estimatesfn)
         }
diff --git a/R/transcriptToGeneExpression.R b/R/transcriptToGeneExpression.R
@@ -15,7 +15,7 @@ transcriptToGeneExpression <- function(se) {
     runnames <- colnames(counts)[-1]
     rowDataSe <- as.data.table(rowData(se))
     
-    counts  = fac2sparse(rowData(se)$GENEID) %*% counts
+    counts  = fac2sparse(factor(rowData(se)$GENEID, levels = unique(rowData(se)$GENEID))) %*% counts
     if(!is.null(metadata(se)$incompatibleCounts)){
         incompatibleCounts <- metadata(se)$incompatibleCounts
         if("nonuniqueCounts" %in% names(metadata(se))){

Original file line number	Diff line number	Diff line change
`@@ -42,7 +42,7 @@ writeBambuOutput <- function(se, path, prefix = "", outputExtendedAnno = TRUE,`
`42`	`42`	`}`
`43`	`43`	`#write incompatible counts`
`44`	`44`	`if(!is.null(metadata(se)$incompatibleCounts)){`
`45`		`- estimates = metadata(se)$incompatibleCounts`
	`45`	`+ estimates <- metadata(se)$incompatibleCounts`
`46`	`46`	`estimatesfn <- paste(transcript_gtffn, "incompatibleCounts.mtx", sep = "")`
`47`	`47`	`Matrix::writeMM(estimates, estimatesfn)`
`48`	`48`	`}`