R/exportEdgeResult.R

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

#' @include AllClasses.R AllGenerics.R AllMethods.R pseudoT.R
NULL

#' Write DGE tables in individual files, and the merged table in one file
#' @param edgeResult An \code{EdgeResult} object
#' @param outdir Output directory
#' @return \code{NULL}, side effects are used
#' @importFrom ribiosIO writeMatrix.tableList writeMatrix
#' @export
writeDgeTables <- function(edgeResult, outdir=getwd()) {
  contrasts <- contrastNames(edgeResult)
  outfiles <- file.path(outdir,
                        sprintf("topTable-%s.txt", contrasts))
  tables <- lapply(contrasts, function(x) dgeTable(edgeResult, x))
  ribiosIO::writeMatrix.tableList(tables, outfiles, row.names=FALSE)
  ribiosIO::writeMatrix(dgeTable(edgeResult),
                        file.path(outdir, "topTable.txt"), row.names=FALSE)
}

#' Write dgeTables with pseudo T statistics
#' @param edgeResult An \code{EdgeResult} object
#' @param outdir Output directory
#' @return \code{NULL}, side effects are used
#' @seealso \code{\link{dgeTableWithPseudoT}}
#' @importFrom ribiosIO writeMatrix.tableList
#' @export
writeDgeTablesWithPseudoT <- function (edgeResult, outdir = getwd()) {
  contrasts <- contrastNames(edgeResult)
  outfiles <- file.path(outdir, sprintf("topTableWithPseudoT-%s.txt", 
                                        contrasts))
  tables <- lapply(contrasts, function(x) dgeTableWithPseudoT(edgeResult, 
                                                   x))
  ribiosIO::writeMatrix.tableList(tables, outfiles, row.names=FALSE)
}

#' Write truncated DGE tables
#' @param edgeResult An \code{EdgeResult} object
#' @param outdir Output directory
#' @return \code{NULL}, side effects are used
#' @importFrom ribiosExpression truncateDgeTable
#' @export
writeTruncatedDgeTables <- function(edgeResult, outdir=getwd()) {
    contrasts <- contrastNames(edgeResult)
    lapply(contrasts, function(x) {
               tbl <- dgeTable(edgeResult, x)
               degs <- ribiosExpression::truncateDgeTable(tbl)
               writeMatrix(degs$pos,
                           file.path(outdir,
                                     sprintf("TruncatedDEGtable-positive-%s.txt", 
                                             x)),
                           row.names=FALSE)
               ribiosIO::writeMatrix(degs$neg,
                           file.path(outdir,
                                     sprintf("TruncatedDEGtable-negative-%s.txt", 
                                             x)),
                           row.names=FALSE)
           })
    return(invisible(NULL))
}

#' Export dgeTest results
#'
#' @param edgeResult A \code{EdgeResult} object
#' @param outRootDir Character string, output directory
#' @param action Character string, what happens if the output directory exists
#'
#' @importFrom ribiosUtils overwriteDir createDir
#' @importFrom ribiosIO writeMatrix
#' @importFrom ribiosExpression writeGct
#' @export
exportEdgeResult <- function(edgeResult, outRootDir,
                             action=c("ask", "append",
                                      "overwrite",
                                      "no")) {
  ow <- ribiosUtils::overwriteDir(outRootDir, action=action)
  if(isFALSE(ow)) {
    return(invisible(NULL))
  }

  ## input data
  inputDir <- file.path(outRootDir, "input-data")
  ribiosUtils::createDir(inputDir)
  countsUnfiltered <- dgeList(edgeResult)$counts.unfiltered
  fDataUnfiltered <- dgeList(edgeResult)$genes.unfiltered

  ribiosExpression::writeGct(countsUnfiltered,
           file.path(inputDir, "counts.gct"))
  ribiosIO::writeMatrix(designMatrix(edgeResult),
              file.path(inputDir, "designMatrix.txt"))
  ribiosIO::writeMatrix(contrastMatrix(edgeResult),
              file.path(inputDir, "contrastMatrix.txt"))
  ribiosIO::writeMatrix(fDataUnfiltered,
              file.path(inputDir, "featureData.txt"))
  ribiosIO::writeMatrix(pData(edgeResult),
              file.path(inputDir, "phenoData.txt"))

  ## filtering
  filterDir <- file.path(outRootDir, "filtered-data")
  ribiosUtils::createDir(filterDir)
  writeGct(counts(edgeResult),
           file.path(filterDir, "filteredCounts.gct"))
  ribiosIO::writeMatrix(fData(edgeResult),
              file.path(filterDir, "filteredFeatureData.txt"))

  ## dge tables
  dgeDir <- file.path(outRootDir, "dgeTables")
  ribiosUtils::createDir(dgeDir)
  writeDgeTables(edgeResult, outdir=dgeDir)

  ## truncated dgeTables
  truncDir <- file.path(outRootDir, "truncated-dgeTables")
  ribiosUtils::createDir(truncDir)
  writeTruncatedDgeTables(edgeResult, outdir=truncDir)

  ## RData
  rdataDir <- outRootDir
  ribiosUtils::createDir(rdataDir)
  save(edgeResult, 
       file=file.path(rdataDir, "ngsDge.RData"))

  ## dgeCounts
  statdir <- file.path(outRootDir, "statistics")
  ribiosUtils::createDir(statdir)
  ribiosIO::writeMatrix(sigGeneCounts(edgeResult), 
              file=file.path(statdir, "ngs-diffGeneCounts.txt"),
              row.names=TRUE)
  lfc <- logFCmatrix(edgeResult)
  lfcPearson <- cor(lfc, use="complete.obs", method="pearson")
  lfcSpearman <- cor(lfc, use="complete.obs", method="spearman")
  ribiosIO::writeMatrix(lfc,
              file=file.path(statdir, "logFCmatrix.txt"))
  ribiosIO::writeMatrix(lfcPearson,
              file=file.path(statdir, "logFCmatrix-PearsonCorrelation.txt"))
  ribiosIO::writeMatrix(lfcSpearman,
              file=file.path(statdir, "logFCmatrix-SpearmanCorrelation.txt"))
}