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

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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.

Author
Daniel Lai, Gavin Ha, Sohrab Shah
Date of publication
None
Maintainer
Daniel Lai <dalai@bccrc.ca>, Sohrab Shah <sshah@bccrc.ca>
License
GPL-3
Version
1.16.0

View on Bioconductor

Man pages

correctReadcount
Readcount correction for GC and mappability bias
HMMcopy-dataset
HMMcopy example dataset
HMMcopy-input
WIG Import Functions
HMMcopy-internal
HMMcopy internal functions
HMMcopy-output
WIG Output Functions
HMMcopy-package
Bias-free copy number estimation and robust CNA detection in...
HMMcopy-visualize
Visualization functions for correctReadcount results
HMMsegment
Segmentation and classification of copy number profiles
wigsToRangedData
Parsing and sorting of uncorrected read and sequence...

Files in this package

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