#' Create necessary folders for pipeline
#'
#' This convenience function automatically creates directories needed
#' for file processing in the pipeline.
#'
#' @param create logical (default FALSE) Whether to create folders in
#' current package directory
#'
#' @return A character vector of created directories
#' @export
dataDirectories <- function(create=FALSE) {
extData <- "inst/extdata/"
clinicalData <- file.path(extData, "Clinical")
directories <- IRanges::CharacterList(
extData = extData,
clinicalData = clinicalData,
curatedSubtypes =
file.path(extData, "curatedSubtypes"),
curatedMaps = file.path(extData, "curatedSubtypes",
"curatedMaps"),
subtypePath = file.path(extData, "allsubtypes"),
clinicalCurationPath =
file.path(extData, "TCGA_Clinical_Curation"),
rawClinical = file.path(clinicalData, "raw"),
basicClinical = file.path(clinicalData, "basic"), enhancedClinical = file.path(clinicalData, "enhanced"),
mergedClinical = file.path(clinicalData, "merged")
)
if (create) {
message("Creating 'inst' directory in ", getwd())
invisible(lapply(directories,
function(folder) {
if (!file.exists(folder))
dir.create(folder, recursive = TRUE)
}
))
}
return(directories)
}
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