R/writeQueryFile.R

In BaderLab/netDx: Network-based patient classifier

#' Wrapper to write GeneMANIA query file
#'
#' @param qSamps (char) vector of patient IDs in query
#' @param incNets (char) vector of networks to include in this analysis
#' (features/pathway names). Useful for subset-based feature selection
#' @param numReturn (integer) number of patients to return in ranking file
#' @param outFile (char) path to output file
#' @param orgName (char) organism name
#' @return No value. Side effect of writing the query file to
#' \code{outFile}
#' @examples
#' data(pheno)
#' writeQueryFile(pheno$ID[seq_len(5)], 'all',nrow(pheno), 'myquery.txt')
#' @export
writeQueryFile <- function(qSamps, incNets = "all", numReturn = 1L, outFile, 
		orgName = "predictor") {
    fileConn <- file(outFile, "w")
    writeLines(sprintf("%s", orgName), con = fileConn)  # org name
    writeLines(sprintf("%s", paste(qSamps, collapse = "\t")), con = fileConn)
    # networks
    writeLines(sprintf("%s", paste(incNets, collapse = "\t")), con = fileConn)
    writeLines(sprintf("%i", numReturn), con = fileConn)  #num2return
    writeLines("automatic", con = fileConn)  # combining
    close(fileConn)
}