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

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

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tar -zxvf

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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]]]))
    	}
    }

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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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#Here is how to convert a bigWig file from hg18 to hg19:

bigWigToBedGraph file18.bw hg18.chrom.sizes chfile18.bed
liftOver file18.bed hg18ToHg19.over.chain file19.bed unmapped
bedGraphToBigWig file19.bed hg19.chrom.sizes file19.bw

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darken <- function(color, factor=1.4){
    col <- col2rgb(color)
    col <- col/factor
    col <- rgb(t(col), maxColorValue=255)
    col
}


lighten <- function(color, factor=1.4){
    col <- col2rgb(color)

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fastq-dump file.sra -Z | gzip > file.fastq.gz

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getR2 <- function(Y,X){
    fitted  <- t(solve(t(X)%*%X) %*% t(X) %*% t(Y)) %*% t(X)
    res     <- Y-fitted
    Y.demeaned <- t(scale(t(Y), center=TRUE, scale=FALSE))
    ssres   <- rowSums(res^2)
    sstot   <- rowSums(Y.demeaned^2)
    1-ssres/sstot
}

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Reduce(intersect, list(a,b,c,d))