Merge pull request #578 from GoekeLab/exportNewFunctions

export generateUniqueCountsSEFromQuantData

Author: lingminhao

NAMESPACE

@@ -6,6 +6,7 @@ export(plotBambu)
 export(prepareAnnotations)
 export(readFromGTF)
 export(transcriptToGeneExpression)
+export(generateUniqueCountsSEFromQuantData)
 export(writeBambuOutput)
 export(writeToGTF)
 export(writeAnnotationsToGTF)

R/bambu-quantify.R

@@ -10,7 +10,7 @@ bambu.quantify <- function(readClassDt, columnIdx, incompatibleCounts, txid.inde
     # Calculate nobs for sample(s) columnIdx
     # Use data.table syntax for in-place creation of nobs column for the scope of this function
     readClassDt[, nobs := {
-        ids <- columnIdx[[1]]
+        ids <- columnIds[[1]]
         if (is.null(ids) || length(ids) == 0 || is.na(ids[1])) {
             0L
         } else if (length(columnIdx) == 1) {

R/transcriptToGeneExpression.R

@@ -62,7 +62,7 @@ transcriptToGeneExpression <- function(se) {
 #' @return A SummarizedExperiment object with \code{assays$uniqueCounts},
 #'   \code{metadata$incompatibleCounts}, and \code{metadata$nonuniqueCounts}
 #' @import data.table
-#' @noRd
+#' @export
 generateUniqueCountsSEFromQuantData <- function(quantData, annotations) {
     uniqueCountsList <- lapply(quantData, function(x) {
         readClassDt <- getReadClassDt(x)