exomeCopy: Copy number variant detection from exome sequencing read depth

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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.

Author
Michael Love
Date of publication
None
Maintainer
Michael Love <michaelisaiahlove@gmail.com>
License
GPL (>= 2)
Version
1.20.0

View on Bioconductor

Man pages

compileCopyCountSegments
Compile segments across samples
copyCountSegments
Segments of identical copy count from exomeCopy
countBamInGRanges
Count reads from BAM file in genomic ranges
exomeCopy
Fit the exomeCopy or exomeCopyVar model to the observed...
ExomeCopy-class
Class "ExomeCopy"
exomeCopy-package
Copy number variant detection from exome sequencing read...
exomecounts
Sample counts from 16 exome sequencing samples from 1000...
generateBackground
Generate median background read depth
getGCcontent
Get the GC content of target ranges from a reference FASTA...
negLogLike
Generalized negative log likelihood and Viterbi algorithms
plotCompiledCNV
Plot compiled CNV segments for one sequence/chromosome
plot.exomeCopyObject
Plot function for exomeCopy
subdivideGRanges
Subdivide ranges of a GRanges object into nearly equal width...

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