plotBAFLRR: BAF-LRR plot

Description Usage Arguments Value Author(s) Examples

View source: R/plotBAFLRR.R

Description

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

Usage

1
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

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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)

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

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