change sampleData to sampleMetadata in assignReadClasstoTranscripts for variable clarity

Author: lingminhao

R/bambu-assignDist.R

@@ -3,7 +3,7 @@
 #' @import data.table
 #' @noRd
 assignReadClasstoTranscripts <- function(readClassList, annotations, isoreParameters, 
-                                        verbose, sampleData, demultiplexed,
+                                        verbose, sampleMetadata, demultiplexed,
                                         returnDistTable = FALSE, trackReads = TRUE) {
     if (is.character(readClassList)) readClassList <- readRDS(file = readClassList)
     metadata(readClassList)$readClassDist <- calculateDistTable(readClassList, annotations, isoreParameters, verbose, returnDistTable)
@@ -17,7 +17,7 @@ assignReadClasstoTranscripts <- function(readClassList, annotations, isoreParame
         mutate(aval = 1) %>%
         data.table()
     #return non-em counts
-    ColData <- generateColData(readClassList, sampleData, demultiplexed)
+    ColData <- generateColData(readClassList, sampleMetadata, demultiplexed)
     quantData <- SummarizedExperiment(assays = SimpleList(
         counts = generateUniqueCounts(readClassDt, metadata(readClassList)$countMatrix, annotations)),
         rowRanges = annotations,

R/bambu.R

@@ -246,7 +246,7 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
                 isoreParameters = isoreParameters, 
                 verbose = verbose, 
                 # for bulk data, there is one sampleData (keep sampleData[1]), for single-cell, there is one per sample
-                sampleData = if(length(sampleData) == 1) sampleData[1] else sampleData[i],
+                sampleMetadata = if(length(sampleData) == 1) sampleData[1] else sampleData[i],
                 demultiplexed = demultiplexed, 
                 returnDistTable = returnDistTable,
                 trackReads = trackReads

R/bambu_utilityFunctions.R

@@ -292,18 +292,18 @@ combineCountSes <- function(countsSe, colDataList, annotations){
     return(combinedCountsSe)
 }
 
-#' Generate the colData using the external sampleData.csv provided by the user in the sampleData argument
+#' Generate the colData using the external sampleMetadata.csv provided by the user in the sampleMetadata argument
 #' @param readClassList A list object containingmetadata about read classes.
-#' @param sampleData A path to a CSV file or NULL/NA if there is no metadata for the sample.
+#' @param sampleMetadata A path to a CSV file or NULL/NA if there is no metadata for the sample.
 #' @param demultiplexed Logical; indicates if data is demultiplexed.
 #'
 #' @return A DataFrame containing colData for the sample.
 #' @export
-generateColData <- function(readClassList, sampleData, demultiplexed) {
-  sampleDataDf <- if (is.null(sampleData) || is.na(sampleData)) {
+generateColData <- function(readClassList, sampleMetadata, demultiplexed) {
+  sampleMetadataDf <- if (is.null(sampleMetadata) || is.na(sampleMetadata)) {
     if (demultiplexed) tibble(barcode = character()) else tibble(sampleName = character())
   } else {
-    read.csv(sampleData)
+    read.csv(sampleMetadata)
   }
   samples <- metadata(readClassList)$samples
   joinKey <- if (demultiplexed) "barcode" else "sampleName"
@@ -317,7 +317,7 @@ generateColData <- function(readClassList, sampleData, demultiplexed) {
   }
 
   colData <- colData %>%
-    left_join(sampleDataDf, by = joinKey) %>%
+    left_join(sampleMetadataDf, by = joinKey) %>%
     as.data.frame()
 
   rownames(colData) <- colData$id