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ExomeDepth (version 0.8.0)

Calls CNV from exome sequence data

Description

Calls copy number variants (CNVs) from targeted sequence data

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Version

Install

install.packages('ExomeDepth')

Monthly Downloads

109

Version

0.8.0

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

April 28th, 2012

Functions in ExomeDepth (0.8.0)

qbetabinom

Quantile for betabin function
getBamCounts

Get count data for multiple exomes
ExomeDepth-package

Read depth based CNV calls for exome DNA sequence data
TestCNV

Computes the Bayes Factor in favour of a CNV defined by position and type.
get.power.betabinom

Estimate the power to compare two beta-binomial distributions.
CallCNVs

Call CNV data from an ExomeDepth object.
ExomeCount

Example dataset for ExomeDepth
qbetabinom.ab

Quantile function for the beta-binomial distribution
exons.hg19

Positions of exons on build hg19 of the human genome
plot-methods

~~ Methods for Function plot ~~
viterbi.hmm

Computes the Viterbi path for a hidden markov model
ExomeDepth-class

Class ExomeDepth
countBamInGRanges.exomeDepth

Compute read count data from BAM files.
select.reference.set

Combine multiple samples to optimize the reference set in order to maximise the power to detect CNV.