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exomeCopy (version 1.18.0)

Copy number variant detection from exome sequencing read depth

Description

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.

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Version

Version

1.18.0

License

GPL (>= 2)

Maintainer

Michael Love

Last Published

February 15th, 2017

Functions in exomeCopy (1.18.0)

getGCcontent

Get the GC content of target ranges from a reference FASTA file
generateBackground

Generate median background read depth
subdivideGRanges

Subdivide ranges of a GRanges object into nearly equal width ranges
exomecounts

Sample counts from 16 exome sequencing samples from 1000 Genomes Project
ExomeCopy-class

Class "ExomeCopy"
compileCopyCountSegments

Compile segments across samples
copyCountSegments

Segments of identical copy count from exomeCopy
exomeCopy

Fit the exomeCopy or exomeCopyVar model to the observed counts.
plotCompiledCNV

Plot compiled CNV segments for one sequence/chromosome
negLogLike

Generalized negative log likelihood and Viterbi algorithms
countBamInGRanges

Count reads from BAM file in genomic ranges
exomeCopy-package

Copy number variant detection from exome sequencing read depth
plot.ExomeCopy

Plot function for exomeCopy