R/writeGisticSummary.R

In maftools: Summarize, Analyze and Visualize MAF Files

#' Writes GISTIC summaries to output tab-delimited text files.
#'
#' @param gistic an object of class \code{GISTIC} generated by \code{readGistic}
#' @param basename basename for output file to be written.
#' @return None. Writes output as tab delimited text files.
#' @seealso \code{\link{readGistic}}
#' @examples
#' all.lesions <- system.file("extdata", "all_lesions.conf_99.txt", package = "maftools")
#' amp.genes <- system.file("extdata", "amp_genes.conf_99.txt", package = "maftools")
#' del.genes <- system.file("extdata", "del_genes.conf_99.txt", package = "maftools")
#' scores.gistic <- system.file("extdata", "scores.gistic", package = "maftools")
#' laml.gistic = readGistic(gisticAllLesionsFile = all.lesions, gisticAmpGenesFile = amp.genes, gisticDelGenesFile = del.genes, gisticScoresFile = scores.gistic)
#' write.GisticSummary(gistic = laml.gistic, basename = 'laml')
#'
#' @export


write.GisticSummary = function(gistic, basename = NULL){

  if(is.null(basename)){
    stop('Please provide a basename for output files.')
  }

  write.table(x = gistic@data, file = paste(basename,'_gisticData.txt', sep=''), sep='\t', quote = FALSE, row.names = FALSE)
  write.table(x = gistic@cnv.summary, file = paste(basename,'_gisticCNVSummary.txt', sep=''), sep='\t', quote = FALSE, row.names = FALSE)
  write.table(x = gistic@cytoband.summary, file = paste(basename,'_gisticCytobandSummary.txt', sep=''), sep='\t', quote = FALSE, row.names = FALSE)
  write.table(x = gistic@gene.summary, file = paste(basename,'_gisticGeneSummary.txt', sep=''), sep='\t', quote = FALSE, row.names = FALSE)
}