R/methods-list.R

In rscharpf/MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

#' @param outdir character string indicating path to save output
#' @aliases calculateMindist,list-method
#' @rdname calculateMindist
setMethod("calculateMindist", signature(object="list"),
	  function(object, outdir=ldPath(), ...){
            pkgs <- neededPkgs()
            if(!isPackageLoaded("ff")){
              foreach(elt=object, .packages=pkgs) %dopar% MinimumDistance:::calculateMindistFromArray(elt, outdir=outdir, ...)
            } else {
              pkgs <- c("ff", pkgs)
              foreach(elt=object, .packages=pkgs) %dopar% MinimumDistance:::calculateMindistFromArray(elt, outdir=outdir, ...)
            }
	  })


unstack <- function(object){
	lrrs <- lapply(object, lrr)
	bafs <- lapply(object, baf)
	new("TrioSetList",
	    assayDataList=AssayDataList(BAF=bafs, logRRatio=lrrs),
	    featureDataList=lapply(object, featureData),
	    phenoData=phenoData(object[[1]]),
	    motherPhenoData=motherPhenoData(object[[1]]),
	    fatherPhenoData=fatherPhenoData(object[[1]]),
	    chromosome=sapply(object, function(x) unique(chromosome(x))))
}