R/MicroarrayPipeline.R

In fboulnois/made: Microarray Analysis of Differential Expression

#' Microarray pipeline
#'
#' Run the full microarray pipeline.
#'
#' Runs the entire microarray pipeline according to the options set in the
#' config. The pipeline consists of quality assessment, normalization,
#' summarization, and creation of the final report.
#'
#' @param config Character string consisting of the path to the configuration
#' file generated using the \code{write.yaml.config} function or parsed
#' configuration list associated with a microarray experiment.
#'
#' @return A character string consisting of the path to the microarray report.
#'
#' @examples
#' if(require(madeData))
#' {
#'   config <- system.file("extdata", "config.yaml", package = "madeData")
#'   ma.pipeline(config)
#' }
#'
#' @seealso \code{\link{write.yaml.config}} to generate the configuration file,
#' \code{\link{ma.normalize}} to perform normalization,
#' \code{\link{ma.summarize}} to perform gene level summarization, and
#' \code{\link{write.report}} to generate the final report including the quality
#' assessment.
#'
#' @export
ma.pipeline <- function(config)
{
  config <- read.yaml.config(config)

  eset <- ma.normalize(config)

  if(config$pipeline$summarization)
  {
    results <- ma.summarize(config, eset)
  }

  if(config$pipeline$write_report)
  {
    report <- write.report(config, eset, results)
  }

  return(report)
}