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CHAT (version 1.1)

getSegChr: Perform binned DNA segmentation by chromosome

Description

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

Usage

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

Arguments

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.

Value

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.

See Also

getSeg

Examples

Run this code
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,])

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