HMMcopy: Copy number prediction with correction for GC and mappability bias for HTS data

Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("HMMcopy")
AuthorDaniel Lai, Gavin Ha, Sohrab Shah
Bioconductor views CopyNumberVariation Microarray Preprocessing Sequencing Visualization
Date of publicationNone
MaintainerDaniel Lai <dalai@bccrc.ca>, Sohrab Shah <sshah@bccrc.ca>
LicenseGPL-3
Version1.18.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/correction.R R/segmentation.R R/zzz.R
build
build/vignette.rds
data
data/tumour.rda
inst
inst/doc
inst/doc/HMMcopy.R
inst/doc/HMMcopy.Rnw
inst/doc/HMMcopy.pdf
inst/extdata
inst/extdata/gc.wig
inst/extdata/map.wig
inst/extdata/normal.wig
inst/extdata/tumour.wig
man
man/HMMcopy-dataset.Rd man/HMMcopy-input.Rd man/HMMcopy-internal.Rd man/HMMcopy-output.Rd man/HMMcopy-package.Rd man/HMMcopy-visualize.Rd man/HMMsegment.Rd man/correctReadcount.Rd man/wigsToRangedData.Rd
src
src/forward_backward.c
src/hmmcopy.h
src/register.c
src/viterbi.c
vignettes
vignettes/HMMcopy.Rnw
vignettes/HMMcopy.bib

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