getAGP: AGP estimation main function

In CHAT: Clonal Heterogeneity Analysis Tool

Description

This function is a wrapper for getSampleAGP() by taking multiple samples and perform batch estimation.

Usage

getAGP(para)

Arguments

para	list, parameters returned from getPara()

Value

A tab-delinimated plain text file with the following fields: sample ID, estimated AGP, (standard deviation), percent genome with CNA, percent on point, percent on regression line, ploidy type, tumor ploidy, overall ploidy, percent of genome amplified, percent of genome deleted, percent of genome with hemizygous deletion, percent of genome with cn-LOH, (95 percent CI lower boundary),(median),(95 percent CI higher boundary).

Author(s)

Bo Li

Examples

data(A0SD.BAF)
data(A0SD.LRR)
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
getAGP(para=para)

CHAT documentation built on May 29, 2017, 10:32 p.m.