getSeg: Perform DNA segmentation and calculate folded BAF and logR ratios.

Description

The function is a wrapper for getSegChr(), which calculates the folded BAF and logR ratios for each chromosome.

Usage

getSeg(BAFfilePath, logRfilePath, sam.col=5, control=TRUE, 
thr.hets=0.1, bin = 500, savefile, data.type='copy',cbs=FALSE,
controlOne=0,nt=FALSE)

Arguments

BAFfilePath

character string, full path to directory where all BAF files are located.

logRfilePath

character string, full path to directory where all LRR files are located.

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 in each bin.

savefile

character string, Rdata file to be saved in working directory.

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.

cbs

if TRUE, circular binary segmentation will be performed using R package 'DNAcopy', instead of binned segmentation.

controlOne

default 0. If assigned, 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.

logical. If true, multi-thread processing is applied. This option is system dependent.

Value

NULL. An Rdata file with variable name 'dd.dat' will be saved in the working directory with following fields: sample-ID, chromosome, start position, end position, LRR value, number of LRR markers, BAF value, number of BAF markers. The saved file can be immediately used in downstream analysis.

Details

The input format for BAF and LRR files are the same and as follows: 1) in the directory, there are n tab-deliminated plain text files, where n is the number of chromosomes, with file name chrN.txt, N=1,2,...22. sex and mitochondria chromosomes are currently not included in the analysis. No other file should be included. 2) for tumor/normal paired design (control=TRUE), each plain text file must have the following fields: Marker-ID, chromosome, start position, end position, Tumor 1, Paired-normal 1, Tumor 2, Paired-normal 2, ..., etc. For study with tumors matched with one control sample, the order of samples is not required. It is not necessary to sort the genomic positions beforehand.

Examples

Run this code

## Not run: 
# 	getSeg(directory_to_BAF_files, directory_to_LRR_files, bin=1000)
# ## End(Not run)