getrefinedpeaks=function(winlist,basecountfile,bpout,peakout,twoBit,winSize,pWinSize=200,printFullOut=0,pquant=0.75,threshold=.01,peakconfidence=0.8,method='pscl',minscore=0, winGap=0, extension=200, FDR=FALSE){
if(!file.exists(winlist)){stop("Specified winlist doesnt exist or is not correct")}
if(!file.exists(basecountfile)){stop("Specified basecountfile doesnt exist or is not correct")}
if(!file.exists(twoBit)){stop("Specified twoBit file doesnt exist or is not correct")}
if(method=='mixture' & FDR==FALSE){
threshold = peakconfidence #need to reconcile this with latest change
}
cat(paste("\nThreshold is ",threshold,"\n",sep=""))
basecountimport(inputfile=basecountfile,winlist=winlist,threshold=threshold,
method=method,printFullOut=printFullOut,outputfile=bpout,
twobitfile=twoBit, winGap=winGap, FDR=FDR)
peakbound(bpprofile=bpout,output=peakout,pwinSize=pWinSize,winSize=winSize,
quantile=pquant,minscore=minscore, extension=extension)
unlink(bpout)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.