CHAT (version 1.1)

plotBAFLRR: BAF-LRR plot

Description

Generate a BAF-LRR plot with thorough annotations of canonical positions and data points.

Usage

plotBAFLRR(sam.dat, cali.best, oo, origin = "on", para = para)

Arguments

sam.dat

numeric matrix, as returned from getSeg() or getSegChr()

cali.best

a list returned from getSumDist()

oo

Origin Cluster, as returned from getOrigin()

origin

if 'on', Origin Cluster will be highlighted on the plot.

para

list, parameters returned from getPara()

Value

NULL

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'
para=getPara()
oo=getOrigin(dd.dat,para=para)
cali=getSampleAGP(dd.dat,oo,para=para)
plotBAFLRR(dd.dat,cali,oo,para=para)