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ExomeDepth (version 0.9.4)

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

0.9.4

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

October 24th, 2012

Functions in ExomeDepth (0.9.4)

ExomeDepth-package

Read depth based CNV calls for exome DNA sequence data

AnnotateExtra-methods

Additional annotations for ExomeDepth objects

plot-methods

~~ Methods for Function plot ~~

AnnotateExtra

Add annotations to a ExomeDepth object

get.power.betabinom

Estimate the power to compare two beta-binomial distributions.

Conrad.hg19.common.CNVs

Conrad et al common CNVs

select.reference.set

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

qbetabinom.ab

Quantile function for the beta-binomial distribution

ExomeDepth-class

Class ExomeDepth

somatic.CNV.call

Call somatic variants between healthy and disease tissues.

initialize-methods

~~ Methods for Function initialize ~~

qbetabinom

Quantile for betabin function

show-methods

~~ Methods for Function show ~~

TestCNV

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

viterbi.hmm

Computes the Viterbi path for a hidden markov model

exons.hg19.X

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

ExomeCount

Example dataset for ExomeDepth

CallCNVs

Call CNV data from an ExomeDepth object.

countBamInGRanges.exomeDepth

Compute read count data from BAM files.

getBamCounts

Get count data for multiple exomes

exons.hg19

Positions of exons on build hg19 of the human genome