R/writeQueryBatchFile.R

In BaderLab/netDx: Network-based patient classifier

#' Write batch.txt file required to create GeneMANIA database
#'
#' @details This file is used to compile features into a single database
#' for feature selection. 
#' @param netDir (char) path to dir with networks
#' @param netList (char) vector of network names
#' @param outDir (char) directory to write batch file
#' @param idFile (char) path to file with patient IDs
#' @param orgName (char) organism name. Don't change the default unless
#' you know what you are doing.
#' @param orgDesc (char) organism description. Similar to \code{orgName},
#' don't change the default
#' @param orgAlias (char) organism alias. Similar to \code{orgName}, don't
#' change the default.
#' @param taxID (integer) taxonomyID required for GeneMANIA . Similar to 
#' \code{orgName}, don't change the default.
#' @return No value. Side effect of writing batch file to 
#' \code{<outDir>/batch.txt}.
#' @export
#' @examples
#' data(npheno)
#' netDir <- system.file("extdata","example_nets",package="netDx")
#' netList <- dir(netDir,pattern='txt$')
#' writeQueryBatchFile(netDir,netList, tempdir(), npheno$ID)
writeQueryBatchFile <- function(netDir, netList, outDir = tempdir(), idFile, 
		orgName = "predictor", 
    orgDesc = "my_predictor", orgAlias = "my_predictor", taxID = 1339) {
    
    outF <- paste(outDir,"batch.txt",sep=getFileSep())
    fileConn <- file(outF, "w")
    
    # organism info
    tmp <- c("#organism", "id", "file", "name", "description", "alias", 
				"taxonomyid")
    tmp2 <- c("organism", basename(idFile), orgName, orgDesc, orgAlias, 
				as.character(taxID))
    writeLines(sprintf("%s", paste(tmp, collapse = "\t")), con = fileConn)
    writeLines(sprintf("%s\n", paste(tmp2, collapse = "\t")), con = fileConn)
    rm(tmp, tmp2)
    
    # group info
    groupName <- "dummy_group"
    groupCode <- "geneset_1"
    groupDesc <- "dummy_group"
    tmp <- c("#group", "name", "code", "description", "RRGGBB colour", 
				"organism")
    tmp2 <- c("group", groupName, groupCode, groupDesc, "ff00ff", orgName)
    writeLines(sprintf("%s", paste(tmp, collapse = "\t")), con = fileConn)
    writeLines(sprintf("%s\n", paste(tmp2, collapse = "\t")), con = fileConn)
    rm(tmp, tmp2)
    
    # network info - header
    tmp <- c("#network", "filename", "name", "description", "group code")
    writeLines(sprintf("%s", paste(tmp, collapse = "\t")), fileConn)
    rm(tmp)
    close(fileConn)
    
    # write networks
    net_DF <- data.frame(type = "network", filename = netList, 
				name = sub(".txt", 
        "", netList), description = netList, groupCode = groupCode)
    write.table(net_DF, file = outF, sep = "\t", col.names = FALSE, 
				row.names = FALSE, 
        quote = FALSE, append = TRUE)
}