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ExomeDepth (version 0.9.2)

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

0.9.2

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

October 20th, 2012

Functions in ExomeDepth (0.9.2)

getBamCounts

Get count data for multiple exomes

ExomeDepth-class

Class ExomeDepth

qbetabinom

Quantile for betabin function

somatic.CNV.call

Call somatic variants between healthy and disease tissues.

CallCNVs

Call CNV data from an ExomeDepth object.

countBamInGRanges.exomeDepth

Compute read count data from BAM files.

exons.hg19.X

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

select.reference.set

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

ExomeCount

Example dataset for ExomeDepth

get.power.betabinom

Estimate the power to compare two beta-binomial distributions.

AnnotateExtra

Add annotations to a ExomeDepth object

initialize-methods

~~ Methods for Function initialize ~~

viterbi.hmm

Computes the Viterbi path for a hidden markov model

show-methods

~~ Methods for Function show ~~

ExomeDepth-package

Read depth based CNV calls for exome DNA sequence data

Conrad.hg19.common.CNVs

Conrad et al common CNVs

exons.hg19

Positions of exons on build hg19 of the human genome

TestCNV

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

plot-methods

~~ Methods for Function plot ~~

qbetabinom.ab

Quantile function for the beta-binomial distribution

AnnotateExtra-methods

Additional annotations for ExomeDepth objects