⚠️There's a newer version (1.1.16) of this package.Take me there.

ExomeDepth (version 0.8.3)

Calls CNV from exome sequence data

Description

Calls copy number variants (CNVs) from targeted sequence data

Copy Link

Version

Install

install.packages('ExomeDepth')

Monthly Downloads

109

Version

0.8.3

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

August 16th, 2012

Functions in ExomeDepth (0.8.3)

initialize-methods

~~ Methods for Function initialize ~~

get.power.betabinom

Estimate the power to compare two beta-binomial distributions.

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.

CallCNVs

Call CNV data from an ExomeDepth object.

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 ~~

qbetabinom

Quantile for betabin function

plot-methods

~~ Methods for Function plot ~~

select.reference.set

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

getBamCounts

Get count data for multiple exomes

ExomeDepth-class

Class ExomeDepth

viterbi.hmm

Computes the Viterbi path for a hidden markov model

qbetabinom.ab

Quantile function for the beta-binomial distribution

ExomeCount

Example dataset for ExomeDepth