R/bgKsTest.R

In dvera/travis: R Utilities for Bed and BEdgRaphs

bgKsTest <- function( bgs , refIndex=NULL , trim=c( 0.05, 0.95 ) , threads=getOption("threads",1L) ){

  bglist=read.bgs(bgs, threads=threads)
  bglist=as.data.frame(lapply(bgl,sort))
  numscores=nrow(bglist)
  numfiles =ncol(bglist)

  if(is.null(refIndex)){
    refscores <- rowMeans(bglist)
  } else{
    refscores <- bglist[,refIndex]
  }

  if(trim[1]!=0){
    startrow=round(trim[1]*numscores)
  } else{ startrow=1}

  if(trim[2]!=1){
    endrow=round(trim[2]*numscores)
  } else{ end=numscores}

  bglist<-bglist[startrow:endrow,]
  stats<-unlist(lapply(1:numfiles,function(x) as.numeric(ks.test(bgl[,x],refscores)$statistic) ) )


}