CHAT (version 1.1)

getPloidy: Genomewide average ploidy

Description

This function returns the genomewide average ploidy of aneuploid fraction and overall of the sample.

Usage

getPloidy(p, type = 1, sam.dat, oo)

Arguments

p

AGP value. see getGrid() for details.

type

integer, ploidy indicator. 1, diploid; 2, tetraploid; 3, hexaploid

sam.dat

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

oo

Origin Cluster, as returned from getOrigin()

Value

Ploidy of the overall sample and ploidy of the aneuploid proportion are returned.

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)
getPloidy(0.5,sam.dat=dd.dat,oo=oo)