falcon {falcon}

Finding Allele-Specific Copy Number in Next-Generation Sequencing Data

Description

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

Author(s)

Hao Chen and Nancy Zhang

Maintainer: Hao Chen ([e-mail])

References

Hao Chen, John Bell, Nicolas Zavala, Hanlee Ji and Nancy Zhang. Allele-specific copy number profiling by next-generation DNA sequencing. Nucleic Acids Research, 2014.

See Also

getChangepoints, getASCN, view

Examples

data(Example) 
# tauhat = getChangepoints(readMatrix)  # uncomment this to run the function. 
 # This example has 6309 variant loci and it took 94 seconds to run on a laptop with 
 # Intel Core i5-2410M processor.
cn = getASCN(readMatrix, tauhat=tauhat)
 # cn$tauhat would give the indices of change-points.  
 # cn$ascn would give the estimated allele-specific copy numbers for each segment.
 # cn$Haplotype[[i]] would give the estimated haplotype for the major chromosome in segment i 
 # if this segment has different copy numbers on the two homologous chromosomes.
view(cn)