diff --git a/NAMESPACE b/NAMESPACE index df261f3a..e9c86d79 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -6,6 +6,7 @@ export(plotBambu) export(prepareAnnotations) export(readFromGTF) export(transcriptToGeneExpression) +export(generateUniqueCountsSEFromQuantData) export(writeBambuOutput) export(writeToGTF) export(writeAnnotationsToGTF) diff --git a/R/bambu-quantify.R b/R/bambu-quantify.R index 65998cad..99f9eaaa 100644 --- a/R/bambu-quantify.R +++ b/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) { diff --git a/R/transcriptToGeneExpression.R b/R/transcriptToGeneExpression.R index a76aa7d0..e39b9c8a 100644 --- a/R/transcriptToGeneExpression.R +++ b/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)