Jfortin1

	extract.portion <- function(file, chr, start, end, verbose = TRUE){
		rl <- IRanges::RangesList(IRanges::IRanges(start=start, end=end))
		names(rl) <- chr
		portion <- import(file, as="Rle",format = "bw", selection = BigWigSelection(rl))
		portion <- portion[chr]
		portion <- as.numeric(portion[[chr]])
		portion
	}

Jfortin1

library(GEOquery)


extractMetaGsm <- function(GEO){
	require(GEOquery)
	GSElimits=NULL
	AnnotGPL=FALSE
	destdir <- tempdir()
	meta <- list()
	for (i in 1:length(GEO)){

Jfortin1

getPCS <- function(matrix, ncomp=2){
  require(mixOmics)
  nipals(matrix, ncomp = ncomp)$p
}

Jfortin1

makeAutosomal <- function(matrix){
    require(IlluminaHumanMethylation450kanno.ilmn12.hg19)
    ann <- getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
    good.probes <- rownames(ann)[-which(ann$chr=="chrX" | ann$chr=="chrY")]
    matrix[rownames(matrix) %in% good.probes,]
}


makeX <- function(matrix){
    require(IlluminaHumanMethylation450kanno.ilmn12.hg19)

Jfortin1

# object must be an RGChannelSet object from the minfi package
getSnpBeta <- function(object){
    require(minfi)
  
    minfi:::.isRG(object)

    manifest <- getManifest(object)
    snpProbesII <- getProbeInfo(manifest, type = "SnpII")$Name

    M.II <- getGreen(object)[getProbeInfo(object, type = "SnpII")$AddressA,]