readMatrix

This is a toy data set we created by taking a subset of the heterozygous SNP sites from data generated by Illumina deep sequencing of a pair of tumor and matched normal samples.  The table has four columns with the column names "AN", "BN", "AT" and "BT", which are the A-allele coverage in the tumor (case) sample, B-allele coverage in the tumor (case) sample, A-allele coverage in the normal (control) sample, and B-allele coverage in the normal (control) sample.  Coverage is defined as simply the number of reads containing the allele among all reads that cover the site.  Each row corresponds to one variant site.  Their corresponding positions in the reference genome are listed in vector "pos" in "Example.rda".  The order of the variant sites is the same order as they appear on the chromosome of the reference genome.  


This is a method for Allele-specific DNA Copy Number Profiling using Next-Generation Sequencing.  Given the allele-specific coverage at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number.  It requires, as input, the read counts for each variant allele in a pair of case and control samples. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual.

readMatrix: An example reads count data

Description

Arguments