Jfortin1

D <- split(as.data.frame(M), A)
correlations <- llapply(D,D,getCorrelation)


llapply <- function(list1,list2, fun){
	temp <- unlist(lapply(list1, function(x){
	unlist(lapply(list2, function(y){
	do.call(fun, list(x,y))
	}))
	}))

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pair.lapply <- function(list1, list2, fun, list3=NULL){
    results <- list()
    for (i in 1:length(list1)){
    	if (is.null(list3)){
    		results[[i]] <- do.call(fun, list(list1[[i]],list2[[i]]))
    	} else {
    		results[[i]] <- do.call(fun, list(list1[[i]][list3[[i]]],list2[[i]][list3[[i]]]))
    	}
    }

Jfortin1

tar -zxvf

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library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
locations <- getLocations(IlluminaHumanMethylation450kanno.ilmn12.hg19)

Jfortin1

killscreens () {
    screen -ls | grep Detached | cut -d. -f1 | awk '{print $1}' | xargs kill
}

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)

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)
}

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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

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

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))
		})