plotBAFLRR: BAF-LRR plot

In Shicheng-Guo/CHAT: Clonal Heterogeneity Analysis Tool

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

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

Shicheng-Guo/CHAT documentation built on Oct. 30, 2019, 11:55 p.m.