falconx: Finding Allele-Specific Copy Number in Whole-Exome Sequencing Data
Version 0.2

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. The implemented method is based on the paper: Chen, H., Jiang, Y., Maxwell, K., Nathanson, K. and Zhang, N. (under review). Allele-specific copy number estimation by whole Exome sequencing.

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AuthorHao Chen and Nancy R. Zhang
Date of publication2017-02-24 23:43:44
MaintainerHao Chen <hxchen@ucdavis.edu>
LicenseGPL (>= 2)
Version0.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("falconx")

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

Functions

ScanBIC2dEM2 Source code
ScanCBS2dEM2 Source code
ScanIterateGrid2dEM2 Source code
biasMatrix Man page
comb Source code
falconx Man page
getASCN.x Man page Source code
getAutoGridSize Source code
getChangepoints.x Man page Source code
hardthres Source code
plotCN Source code
pos Man page
pruning Source code
readMatrix Man page
tauhat Man page
view Source code
view} \title{Viewing Data with Allele-specific Copy Number Man page

Files

src
src/registerDynamicSymbol.c
src/falconx.c
NAMESPACE
data
data/Example.rda
R
R/falconx_sub.r
R/script_basic.r
R/falconx.r
MD5
DESCRIPTION
man
man/tauhat.Rd
man/pos.Rd
man/readMatrix.Rd
man/getASCN.x.Rd
man/getChangepoints.x.Rd
man/falconx.Rd
man/biasMatrix.Rd
man/view.Rd
falconx documentation built on May 19, 2017, 10:59 a.m.