mainProf<-function(file="/home/agriffith/Dropbox/UTX-Alex/jan/combined_sorted.bed",
rawdata=rep(file,22),
n=0){
Rprof("temp.prof")
data<-hg19Sort(loadBedFile(file))
score<-pileUp(data,rawdata,n=n)
print(str(score))
Rprof(NULL)
summaryRprof("temp.prof")}
testHeights<-function(){
file<-"/home/griffita/Dropbox/UTX-Alex/jan/combined_sorted.bed"
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)
dev.off()}
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