R/saveRTCGAdata.R

In waldronlab/MultiAssayExperiment.TCGA: Pipeline for the integration of multi-omics experiments in Bioconductor

#' A function to save data from RTCGAToolbox
#'
#' Saves intermediate data from the GDAC Firehose pipeline via RTCGAToolbox
#'
#' @param runDate The GDAC Firehose run date, only '20160128' is available
#' @param diseaseCode A single string indicating TCGA cancer code
#' @param dataType A character vector indicating the assay type(s)
#' @param analyzeDate The GDAC Firehose analyze run date, only '20160128' is
#' available
#' @param drectory A single string indicating the directory in which to save
#' intermediary datasets
#' @param rawDir Directory location where to save data from the
#' `RTCGAToolbox::getFirehoseData` function
#' @param force logical (default FALSE) whether to force redownload of
#' resources
#'
#' @export
saveRTCGAdata <- function(runDate = "20160128", diseaseCode,
    dataType = c("RNASeqGene", "RNASeq2Gene", "miRNASeqGene",
    "RNASeq2GeneNorm", "CNASNP", "CNVSNP", "CNASeq", "CNACGH", "Methylation",
    "Mutation", "mRNAArray", "miRNAArray", "RPPAArray", "GISTIC"),
    analyzeDate = "20160128", directory, rawDir = "tmp", force = FALSE)
{
    if (!dir.exists(file.path(directory, diseaseCode)))
        dir.create(file.path(directory, diseaseCode), recursive = TRUE)
    choices <- match.arg(dataType, c("RNASeqGene", "RNASeq2Gene",
        "miRNASeqGene", "RNASeq2GeneNorm", "CNASNP", "CNVSNP", "CNASeq",
        "CNACGH", "Methylation", "Mutation", "mRNAArray", "miRNAArray",
        "RPPAArray", "GISTIC"), several.ok = TRUE)
    for(dataType in choices) {
        rdsPath <- file.path(directory, diseaseCode, paste0(diseaseCode, "_",
            dataType, "-", runDate, ".rds"))
        if (!file.exists(rdsPath) || force) {
            gistic <- grepl("^GIST", dataType, ignore.case = TRUE)
            if (gistic) {
                dateType <- "gistic2Date"
                args <- list(analyzeDate, TRUE)
                names(args) <- c(dateType, dataType)
            } else {
                dateType <- "runDate"
                args <- list(runDate, TRUE)
                names(args) <- c(dateType, dataType)
            }
            message("Obtaining data with RTCGAToolbox::getFirehoseData...")
                dataPiece <- do.call(
                    RTCGAToolbox::getFirehoseData,
                    args = c(
                        list(
                            dataset = diseaseCode,
                            miRNASeqGeneType = "reads_per_million_miRNA_mapped",
                            RNAseq2Norm = "RSEM_normalized_log2",
                            clinical = FALSE, destdir = rawDir,
                            forceDownload = force, fileSizeLimit = Inf
                        ),
                        args
                    )
                )
                if (identical(dataType, "miRNASeqGene"))
                    dataPiece@miRNASeqGene <- log2(dataPiece@miRNASeqGene)
                saveRDS(dataPiece, file = rdsPath, compress = "bzip2")
                message(basename(rdsPath), " saved in ", dirname(rdsPath))
        } else { message(diseaseCode, "_", dataType, " data exists") }
    }
}