falconx: Finding Allele-Specific Copy Number in Whole-Exome Sequencing Data

This is a method for Allele-specific DNA Copy Number profiling for whole-Exome sequencing data. Given the allele-specific coverage and site biases 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, as well as the site biases. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual.

Author
Hao Chen and Nancy R. Zhang
Date of publication
2016-04-21 22:13:02
Maintainer
Hao Chen <hxchen@ucdavis.edu>
License
GPL (>= 2)
Version
0.1

View on CRAN

Man pages

biasMatrix
Bias Matrix
falconx
Finding Allele-Specific Copy Number in Whole-Exome Sequencing...
getASCN.x
Getting Allele-specific DNA Copy Number
getChangepoints.x
Getting Change-points
pos
Position (bp)
readMatrix
Reads Matrix
tauhat
Estimated Break Points
view
Viewing Data with Allele-specific Copy Number

Files in this package

falconx
falconx/src
falconx/src/falconx.c
falconx/NAMESPACE
falconx/data
falconx/data/Example.rda
falconx/R
falconx/R/falconx_sub.r
falconx/R/script_basic.r
falconx/R/falconx.r
falconx/MD5
falconx/DESCRIPTION
falconx/man
falconx/man/tauhat.Rd
falconx/man/pos.Rd
falconx/man/readMatrix.Rd
falconx/man/getASCN.x.Rd
falconx/man/getChangepoints.x.Rd
falconx/man/falconx.Rd
falconx/man/biasMatrix.Rd
falconx/man/view.Rd