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

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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.

Author
Hao Chen and Nancy R. Zhang
Date of publication
2016-04-21 08:20:42
Maintainer
Hao Chen <hxchen@ucdavis.edu>
License
GPL (>= 2)
Version
0.2

View on CRAN

Man pages

falcon
Finding Allele-Specific Copy Number in Next-Generation...
getASCN
Getting Allele-specific DNA Copy Number
getChangepoints
Getting Change-points
pos
Position (bp)
readMatrix
An example reads count data
tauhat
Estimated Break Points
view
Viewing Data with Allele-specific Copy Number

Files in this package

falcon
falcon/src
falcon/src/falcon.c
falcon/NAMESPACE
falcon/data
falcon/data/Example.rda
falcon/R
falcon/R/falcon_sub.r
falcon/R/script_basic.r
falcon/R/falcon.r
falcon/MD5
falcon/DESCRIPTION
falcon/man
falcon/man/tauhat.Rd
falcon/man/pos.Rd
falcon/man/getASCN.Rd
falcon/man/readMatrix.Rd
falcon/man/falcon.Rd
falcon/man/getChangepoints.Rd
falcon/man/view.Rd