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ExomeDepth (version 0.9.7)

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

0.9.7

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

December 11th, 2012

Functions in ExomeDepth (0.9.7)

exons.hg19.X

Positions of exons on build hg19 of the human genome and on chromosome X

AnnotateExtra-methods

Additional annotations for ExomeDepth objects

get.power.betabinom

Estimate the power to compare two beta-binomial distributions.

TestCNV

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

plot-methods

~~ Methods for Function plot ~~

qbetabinom

Quantile for betabin function

ExomeDepth-class

Class ExomeDepth

ExomeCount

Example dataset for ExomeDepth

viterbi.hmm

Computes the Viterbi path for a hidden markov model

countBamInGRanges.exomeDepth

Compute read count data from BAM files.

somatic.CNV.call

Call somatic variants between healthy and disease tissues.

CallCNVs

Call CNV data from an ExomeDepth object.

Conrad.hg19.common.CNVs

Conrad et al common CNVs

exons.hg19

Positions of exons on build hg19 of the human genome

qbetabinom.ab

Quantile function for the beta-binomial distribution

ExomeDepth-package

Read depth based CNV calls for exome DNA sequence data

getBamCounts

Get count data for multiple exomes

show-methods

~~ Methods for Function show ~~

initialize-methods

~~ Methods for Function initialize ~~

AnnotateExtra

Add annotations to a ExomeDepth object

select.reference.set

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