#‘ Fetch the TCGA Transcriptome Profiling data
#'
#' This function is used to fetch the TCGA data using TCGABiolink package
#'
#' @param tcga_type TCGA cancer type to download
#' @param download_location location of download file
#' @param data_type default "Gene Expression Quantification"
#' @param workflow_type "HTSeq - FPKM-UQ"
#' @param sample_type "Primary Tumor"
#' @return GDCprepare objects that can be further used for get exp matrix
#' @export
#'
fetch_tcga_data <- function(tcga_type,
download_location,
data_type = "Gene Expression Quantification",
workflow_type = "HTSeq - FPKM-UQ",
sample_type = "Primary Tumor"){
g_query_tumor <- TCGAbiolinks::GDCquery(project = paste0("TCGA-", tcga_type),
data.category = "Transcriptome Profiling",
legacy = F,
data.type = data_type,
workflow.type = workflow_type,
sample.type = sample_type)
TCGAbiolinks::GDCdownload(g_query_tumor,
directory = paste0(download_location, "/", tcga_type, "_tumor"))
tumor <- TCGAbiolinks::GDCprepare(g_query_tumor, save = FALSE,
directory = paste0(download_location, "/", tcga_type, "_tumor"))
return(tumor)
}
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