getPloidy: Genomewide average ploidy

In CHAT: Clonal Heterogeneity Analysis Tool

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.

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

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