pileUp: PileUp

In alexjgriffith/mulcal: To facilitate the analysis of multiple ChIP-Seq data sets

Description

Generates a pile up matrix from a unified set of peaks and a list of raw data sets

Usage

pileUp(data, rawdata, n = 0)

Arguments

data	A preloaded bed data.frame which includes slots $chro $start $end
rawdata	a list of raw data files
n	the number of nodes to use. If 0 then the parrallel package is not used

Author(s)

Alexander Griffith [e-mail]

Source

https://github.com/alexjgriffith/mulcal

Examples

cats<-read.table("/home/griffita/Dropbox/UTX-Alex/jan/catagories")
   prefix<-"/mnt/brand01-00/mbrand_analysis/data_sets/"
   suffix<-"_sorted.bed"
   rawdata<-apply(cats,1,function(x){paste(prefix,x,"/",x,suffix,sep="")})
   data<-hg19Sort(loadBedFile(file))
   score<-pileUp(data,rawdata,n=22)
   temp<-cor(score)
   rownames(temp)<-t(cats)
   colnames(temp)<-t(cats)
   pdf("test.pdf")
   plot(hclust(dist(temp)),hang=-1)

   binSize=10000
   regions<-do.call(rbind, apply(read.table("/data/binaries/BEDTools/genomes/human.hg19.genome")[1:24,],1, function(x,step) {y<-seq(1,as.numeric(x[2]),step); cbind(as.character(x[1]),as.character(y),as.character(y+step))} ,binSize))
  data<-hg19Sort(data.frame(chro=regions[,1],start=as.integer(regions[,2]), end=as.integer(regions[,3])))
  score<-pileUp(data,rawdata,n=22)

alexjgriffith/mulcal documentation built on May 10, 2019, 8:53 a.m.