R/runEstimate.R

In steveneschrich/saeAffy: A Collection of Utilities for Gene Expression Biomarkers.

#' Run the ESTIMATE algorithm on an ExpressionSet, and return the result as
#' an ExpressionSet.
#'
#' @param eset An affy gene expression dataset.
#' @param gene_symbols A list of gene symbols (if not supplied in annotation for ExpressionSet).
#' @return An expression set consisting of estimate scores.
#' @export
#'
#' @examples
#' estimate_scores<-runEstimate(eset)
runEstimate<-function(eset, platform, ...) {
  require(estimate)
  stopifnot(class(eset)=="ExpressionSet")

  if (missing(platform)) platform<-"affymetrix"

  # Transform the eset to index by gene symbol
  eset_bygene<-getExpressionSetByGeneSymbol(eset, ...)
  eset_common_genes<-featureSubset(eset_bygene, estimate::common_genes$GeneSymbol)

    # Estimate is file-based
  estimate_exprs_in_file <- tempfile(pattern="estimate", fileext=".gct")
  writeGCT(eset_common_genes, estimate_exprs_in_file)

  estimate_scores_file <-tempfile(pattern="estimate-out", fileext=".gct")
  estimateScore(input.ds=estimate_exprs_in_file,
                output.ds=estimate_scores_file,
                platform=platform)

  results<-readGCT(estimate_scores_file)

  # At the moment, estimateScore converts to a data.frame inside of it, thereby
  # bashing sample names (if they are not valid). We just replace the sample
  # names with the initial ones.
  sampleNames(results)<-sampleNames(eset)

  return(results)
}