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.

AuthorDaniel Lai, Gavin Ha, Sohrab Shah
Date of publicationNone
MaintainerDaniel Lai <dalai@bccrc.ca>, Sohrab Shah <sshah@bccrc.ca>
LicenseGPL-3
Version1.16.0

View on Bioconductor

Files

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

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