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ExomeDepth (version 0.8.4)

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

0.8.4

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

August 24th, 2012

Functions in ExomeDepth (0.8.4)

ExomeDepth-class

Class ExomeDepth

qbetabinom

Quantile for betabin function

somatic.CNV.call

Call somatic variants between healthy and disease tissues.

qbetabinom.ab

Quantile function for the beta-binomial distribution

select.reference.set

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

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.

countBamInGRanges.exomeDepth

Compute read count data from BAM files.

ExomeDepth-package

Read depth based CNV calls for exome DNA sequence data

show-methods

~~ Methods for Function show ~~

CallCNVs

Call CNV data from an ExomeDepth object.

initialize-methods

~~ Methods for Function initialize ~~

exons.hg19

Positions of exons on build hg19 of the human genome

viterbi.hmm

Computes the Viterbi path for a hidden markov model

getBamCounts

Get count data for multiple exomes

ExomeCount

Example dataset for ExomeDepth

plot-methods

~~ Methods for Function plot ~~