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ExomeDepth (version 0.9.1)

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

0.9.1

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

October 19th, 2012

Functions in ExomeDepth (0.9.1)

Conrad.hg19.common.CNVs

Conrad et al common CNVs

getBamCounts

Get count data for multiple exomes

viterbi.hmm

Computes the Viterbi path for a hidden markov model

initialize-methods

~~ Methods for Function initialize ~~

AnnotateExtra

Add annotations to a ExomeDepth object

qbetabinom

Quantile for betabin function

plot-methods

~~ Methods for Function plot ~~

CallCNVs

Call CNV data from an ExomeDepth object.

TestCNV

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

exons.hg19

Positions of exons on build hg19 of the human genome

countBamInGRanges.exomeDepth

Compute read count data from BAM files.

AnnotateExtra-methods

Additional annotations for ExomeDepth objects

show-methods

~~ Methods for Function show ~~

ExomeDepth-class

Class ExomeDepth

somatic.CNV.call

Call somatic variants between healthy and disease tissues.

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

exons.hg19.X

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

ExomeDepth-package

Read depth based CNV calls for exome DNA sequence data

qbetabinom.ab

Quantile function for the beta-binomial distribution

get.power.betabinom

Estimate the power to compare two beta-binomial distributions.