getSegChr: Perform binned DNA segmentation by chromosome
In CHAT: Clonal Heterogeneity Analysis Tool

Description Usage Arguments Value Author(s) See Also Examples

This function computes folded BAF and logR ratios for binned DNA segments for a given chromosome.

1 2	getSegChr(bb.chr = NULL, ll.chr = NULL, sam.col=5, control=TRUE, thr.hets=0.1, bin = 1000, data.type='copy',controlOne=0)

`bb.chr`	numeric matrix, original B-allele frequency for a given chromosome for all samples.
`ll.chr`	numeric matrix, original logR ratio for a given chromosome for all samples.
`sam.col`	the index of the column in BAF or LRR files where the first sample starts
`control`	If TRUE, each tumor sample is paired with normal immediately after it. The columns of the data file is organized : sample_1, control_1, sample_2, control_2 .... If FALSE, each sample serves the control of itself.
`thr.hets`	lower threshold of calling homozygous markers. BAF<=thr.hets or BAF>=1-thr.hets are considered homozygous.
`bin`	integer, number of markers contained in each bin.
`data.type`	character string chosen from c('copy', 'log'). If 'copy', the value for LRR markers represent the copy number of SNPs. If 'log', the value is log2 based copy number intensity.
`controlOne`	default 0. If positive, must be an integer number indicating the index of one control sample in the sample list. This control will be used for all the samples.

a matrix containing the following columns: chromosome, start position, end position, median LRR value, number of LRR markers, folded BAF value, number of germline heterozygous BAF markers, with row names being sample ID.

Bo Li

getSeg

library(CHAT)
data(A0SD.BAF)
data(A0SD.LRR)
CHR=8
chr8.baf=A0SD.BAF[which(A0SD.BAF[,2]==CHR),]
chr8.lrr=A0SD.LRR[which(A0SD.LRR[,2]==CHR),]
dd=getSegChr(chr8.baf,chr8.lrr)
print(dd[1:4,])

Loading required package: parallel
Loading required package: DNAcopy
Loading required package: DPpackage
 
DPpackage 1.1-7.4
 
Copyright (C) 2006 - 2012, Alejandro Jara
Department of Statistics
P.U. Catolica de Chile
 
Support provided by Fondecyt
11100144 grant.
 
processing  8 
............................     id                 chr                       logR.mean            bin   
[1,] "TCGA.A1.A0SD.01A" "8" "220007"   "5366616"  "0.0652276227756192" "1000"
[2,] "TCGA.A1.A0SD.01A" "8" "5370001"  "11082559" "0.0731347046302153" "1000"
[3,] "TCGA.A1.A0SD.01A" "8" "11083792" "18487665" "0.065572311593622"  "1000"
[4,] "TCGA.A1.A0SD.01A" "8" "18488803" "26866779" "0.0932221105390241" "1000"
     BAF.mean             bin   
[1,] "0.021610357244357"  "1000"
[2,] "0.0215504612180461" "1000"
[3,] "0.0258134550412758" "1000"
[4,] "0"                  "1000"