#' Generate QC Metrics for a given dataset.
#'
#' There are a number of different packages and routines that generate
#' various QC metrics for an Affy array. This function calls each of them
#' to generate a list of QC metrics that can be used to graph or otherwise
#' output information on.
#'
#' @param name The name of the dataset.
#' @param path Path to the celfiles for the dataset.
#'
#' @return A list of objects representing different QC approaches.
#' @export
#'
#' @examples
generate_QCMetrics<-function(name, path) {
requireNamespace("affy")
requireNamespace("simpleaffy")
requireNamespace("yaqcaffy")
message(sprintf("%s: Loading CEL files as affybatch.", name))
abatch<-affy::read.affybatch(list.celfiles(path, full.names=TRUE))
message(sprintf("%s: Generate Affy RNA Degradation result.", name))
affyrnadeg<-affy::AffyRNAdeg(abatch)
message(sprintf("%s: Generate simpleaffy result.", name))
simpleaffy<-simpleaffy::qc(abatch)
message(sprintf("%s: Generate YAQC result.", name))
yaqc<-yaqcaffy::yaqc(abatch, verbose=TRUE)
list(affybatch = abatch,
affyrnadeg = affyrnadeg,
simpleaffy = simpleaffy,
yaqc = yaqc,
name = name)
}
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