R/getRseTx.R

In JMF47/recountNNLS: Transcript abundance linear modeling from compressed coverage information

#' Download and/or access quantified SRA projects
#'
#' This function downloads and/or loads into R a
#' \code{rangedSummarizedExperiment} object for transcript level abundance
#' produced by the latest version of recountNNLS.
#' @param project A SRA project name for a project already curated in recount2.
#' @param download_path Where the rse should be downloaded to if not NULL.
#' @param tissue A specific tissue type of interest. Relevant only to TCGA
#' and GTEX (SRP012682) samples. Defaults to NULL.
#' Defaults to NULL, i.e. no downloading.
#' @return Returns the path to downloaded object.
#' @examples
#' project = 'DRP000366'
#' getRseTx(project)
#' @keywords recountNNLS
#' @import SummarizedExperiment
#' @export
getRseTx = function(project, tissue=NULL, download_path=paste0(getwd(), '/rse_tx.RData')){
      if(project %in% c('TCGA', 'SRP012682') & (!is.null(tissue))){
            target = paste0('http://duffel.rail.bio/recount/v2/', project, '/rse_tx_', tissue, '.Rdata')
      }else{
            target = paste0('http://duffel.rail.bio/recount/v2/', project, '/rse_tx.RData')
      }
      download.file(url=target, destfile=download_path)
      return(download_path)
}