saveMapData <- function(
data_list, clinical_frame, FUN = TCGAutils::TCGAbarcode,
cancer, force, directory
) {
sampMap <- generateMap(data_list, clinical_frame, FUN)
splitMap <- splitAsList(sampMap, sampMap[["assay"]])
mapDir <- file.path(directory, cancer)
if (!dir.exists(mapDir))
dir.create(mapDir, recursive = TRUE)
mapFiles <- list.files(path = mapDir, pattern = "_map.csv",
full.names = TRUE)
assayNames <- gsub("_map.csv", "", basename(mapFiles))
splitNames <- if (force) TRUE else { !names(splitMap) %in% assayNames }
newAssays <- names(splitMap)[splitNames]
for (assay in newAssays)
write.table(splitMap[[assay]], sep = ",",
file = file.path(mapDir, paste0(assay, "_map.csv")))
return(sampMap)
}
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