exomeCopy: Copy number variant detection from exome sequencing read depth

Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

AuthorMichael Love
Date of publicationNone
MaintainerMichael Love <michaelisaiahlove@gmail.com>
LicenseGPL (>= 2)
Version1.20.0

View on Bioconductor

Files in this package

exomeCopy/DESCRIPTION
exomeCopy/NAMESPACE
exomeCopy/NEWS
exomeCopy/R
exomeCopy/R/classes.R exomeCopy/R/helper_functions.R exomeCopy/R/main_functions.R exomeCopy/R/methods.R
exomeCopy/build
exomeCopy/build/vignette.rds
exomeCopy/data
exomeCopy/data/exomecounts.rda
exomeCopy/inst
exomeCopy/inst/doc
exomeCopy/inst/doc/exomeCopy.R
exomeCopy/inst/doc/exomeCopy.Rnw
exomeCopy/inst/doc/exomeCopy.pdf
exomeCopy/inst/extdata
exomeCopy/inst/extdata/1000Genomes_files.txt
exomeCopy/inst/extdata/mapping.bam
exomeCopy/inst/extdata/mapping.bam.bai
exomeCopy/inst/extdata/mapping.sam
exomeCopy/inst/extdata/reference.fa
exomeCopy/inst/extdata/reference.fa.fai
exomeCopy/inst/extdata/targets.bed
exomeCopy/man
exomeCopy/man/ExomeCopy-class.Rd exomeCopy/man/compileCopyCountSegments.Rd exomeCopy/man/copyCountSegments.Rd exomeCopy/man/countBamInGRanges.Rd exomeCopy/man/exomeCopy-package.Rd exomeCopy/man/exomeCopy.Rd exomeCopy/man/exomecounts.Rd exomeCopy/man/generateBackground.Rd exomeCopy/man/getGCcontent.Rd exomeCopy/man/negLogLike.Rd exomeCopy/man/plot.exomeCopyObject.Rd exomeCopy/man/plotCompiledCNV.Rd exomeCopy/man/subdivideGRanges.Rd
exomeCopy/src
exomeCopy/src/exomeCopy.c
exomeCopy/vignettes
exomeCopy/vignettes/exomeCopy.Rnw
exomeCopy/vignettes/exomeCopy.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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