## Not run:
# ## This is not executable. User must create their own VCF directory.
# id='TCGA.A1.A0SD'
# VCFdir='VCF/'
# ## Slow. Run with caution.
# data(A0SD.BAF)
# data(A0SD.LRR)
# ## DNA segmentation
# seg.dat=c()
# for(CHR in c(8,9,10)){
# baf=A0SD.BAF[A0SD.BAF[,2]==CHR,]
# lrr=A0SD.LRR[A0SD.LRR[,2]==CHR,]
# x=getSegChr(baf,lrr)
# seg.dat=rbind(seg.dat,x)
# }
# dd.dat=seg.dat[,2:8]
# rownames(dd.dat)=seg.dat[,1]
# mode(dd.dat)='numeric'
# save(dd.dat,file='A0SDseg.Rdata')
# para=getPara()
# para$datafile='A0SDseg.Rdata'
# para$savefile='A0SD-AGP.txt'
# para$is.normalize=FALSE
# ## AGP estimation
# getAGP(para=para)
# para.s=getPara.sAGP()
# para.s$inputdata='A0SDseg.Rdata'
# para.s$purityfile='A0SD-AGP.txt'
# para.s$savedata='A0SD-sAGP.Rdata'
# ## sAGP estimation
# getsAGP(para=para.s)
# load('A0SD-sAGP.Rdata')
# getSampleCCF(id,new.dd,VCFdir)
# ## End(Not run)
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