CHAT (version 1.1)

MergeBreakPointsByChr: Merge break points from two sets

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.

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)