getPermutation: Null distribution for estimated AGP.

In Shicheng-Guo/CHAT: Clonal Heterogeneity Analysis Tool

Description

This function performs weighted bootstrap on segmentation data to obtain null distribution of estimated AGP.

Usage

getPermutation(sam.dat, oo, Np = 100, type = 1, para)

Arguments

sam.dat	numeric matrix, as returned from getSeg() or getSegChr()
oo	Origin Cluster, as returned from getOrigin()
Np	integer, number of bootstraps.
type	integer, ploidy indicator. 1, diploid; 2, tetraploid; 3, hexaploid
para	list, parameters returned from getPara()

Value

A numeric vector containing all the bootstrap AGP values from Np times of resampling.

Author(s)

Bo Li

Examples

## Slow. Run with caution.

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)
p.null=getPermutation(dd.dat,oo,para=para)

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