getSampleAGP: AGP inference by sample

In Shicheng-Guo/CHAT: Clonal Heterogeneity Analysis Tool

Description

This function performs AGP inference based on canonical positions on BAF-LRR plot for one sample.

Usage

getSampleAGP(sam.dat, oo, para)

Arguments

sam.dat	numeric matrix, as returned from getSeg() or getSegChr()
oo	Origin Cluster, as returned from getOrigin()
para	list, parameters returned from getPara()

Details

AGP values and possible ploidy types of the input sample are screened for best combination which minimizes the total summation of distances from observed data points to the grid of theoretical canonical positions.

Value

A list inherited from the output of getSumDist() with additional elements:

percent.on.track	For quality control, percent of genome close to at least one regression line.
percent.on.point	For quality control, percent of genome close to at least one canonical point.
percent.change	For quanlity control, percent of genome with CNA.
sam.p	estimated AGP of the sample
type	estimated ploidy type of the sample

If is.perm is set TRUE in para, additional elements are included:

conf.int	95 percent confident interval of estimated AGP
std	standard deviation of estimated AGP

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)
getSampleAGP(dd.dat,oo,para=para)

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