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splitByRow <- function(Y, f){
	require(tidyverse)
	names <- dimnames(Y)
	Y <- as.matrix(Y); dimnames(Y) <- names
	#levels <- sort(unique(f)) %>% as.character
	temp <- split(Y, f=f)
	names <- names(temp)
	ns <- table(f)[names]
	temp <- lapply(1:length(temp), function(i){
		x <- matrix(temp[[i]], ncol=ncol(Y), nrow=ns[[i]], byrow=FALSE)

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tstat.ord <- fit$coef / fit$stdev.unscaled / fit$sigma

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ComBat2 <- function(dat, batch, mod=NULL, par.prior=TRUE,prior.plots=FALSE,mean.only=FALSE,ref.batch=NULL, verbose=FALSE) {
  # make batch a factor and make a set of indicators for batch
  require(sva)
  if(mean.only==TRUE){
    cat("Using the 'mean only' version of ComBat\n")
  }
  if(length(dim(batch))>1){
    stop("This version of ComBat only allows one batch variable")
  }  ## to be updated soon!
  batch <- as.factor(batch)

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getMNITemplatePath <- function(what=c("full", "brain", "brain_mask"), res=c("1mm", "2mm")){
	require(fslr)
	dir <- file.path(fsl_data_dir(), "standard")
	what <- match.arg(what)
	res  <- match.arg(res)
    if (what == "full") {
        file <- file.path(dir, paste0("MNI152_T1_",res,".nii.gz"))
    }
    else if (what == "brain") {
        file <- file.path(dir, paste0("MNI152_T1_",res,"_brain.nii.gz"))

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# Wrapper to calculate t-statistic from vash with one covariate
getVashT <- function(x, mod, df=NULL, ...){
  require(vashr)
  require(limma)
  fit <- lmFit(x, mod)
  if (is.null(df)){
    df <- ncol(x)-1
  }
  temp <- vash(sehat = fit$sigma,  df=df, ...)
  temp <- fit$coef[,2] / temp$sd.post / fit$stdev.unscaled[,2]

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

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

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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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#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