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,]

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

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

Jfortin1

library(GEOquery)


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

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

extract.block <- function(files, chr, start, end, verbose = TRUE){
		rl <- IRanges::RangesList(IRanges::IRanges(start=start, end=end))
		names(rl) <- chr
		cat("[extract.block] Reading in the files \n")
		rles <- lapply(files, function(xx) {
			#if (verbose){
			#	cat("Reading", xx, "\n")
			#}
	    	import(xx, as = "Rle", format = "bw", selection = BigWigSelection(rl))
		})

Jfortin1

library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
ann <- getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
island.status <- gsub("N_|S_","",ann$Relation_to_Island)
counts <- table(island.status)
percs <- counts/nrow(ann)*100

Jfortin1

impute.matrix <- function (matrix) {
	missing <- which(is.na(matrix) | !is.finite(matrix), arr.ind=TRUE)
	if (length(missing)!=0){
		for (j in 1:nrow(missing)){
				mean <- mean(matrix[missing[j,1],][is.finite(matrix[missing[j,1],])], na.rm=TRUE)
				matrix[missing[j,1],missing[j,2]] <- mean
			}
	}
  	matrix
}

Jfortin1

BetaToM <- function(beta){
  matrix <- log2(beta) - log2(1-beta)
  impute.matrix(matrix)
}

MToBeta <- function(mmatrix){
  matrix <- 2^mmatrix/(2^mmatrix+1)
  impute.matrix(matrix)
}

Jfortin1

# To ask for more writing memory:
-l h_fsize=40G

# Tar

tar -xvfz

# To remove all deleted files from git repo: 
git rm $(git ls-files --deleted)