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#' @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))))
}
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