MergeBreakPointsByChr: Merge break points from two sets

In CHAT: Clonal Heterogeneity Analysis Tool

Description

Two sets of break points from one chromosome, typically from B-allele frequency and logR ratios respectively are inputs, and this function merges the two sets as one.

Usage

MergeBreakPointsByChr(chr, id, seg.B, seg.L, map.chr, thr = 5)

Arguments

chr	chromosome number
id	sample identifier
seg.B	segmentation matrix for BAF as returned by segment() from 'DNAcopy'
seg.L	segmentation matrix for LRR as returned by segment() from 'DNAcopy'
map.chr	SNP positions or starting position of aCGH markers.
thr	if two break points are located within thr number of markers, they will be merged.

Value

a new matrix with merged segmentations.

Author(s)

Bo Li

Examples

seg.L<-cbind('temp',1,matrix(c(1,10,11,100,101,120),ncol=2,byrow=TRUE))
seg.B<-cbind('temp',1,matrix(c(1,11,12,60,61,120),ncol=2,byrow=TRUE))
map.chr<-1:130
MergeBreakPointsByChr(1,'temp',seg.B,seg.L,map.chr)

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