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

ExomeDepth (version 0.9.8)

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

0.9.8

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

December 11th, 2013

Functions in ExomeDepth (0.9.8)

AnnotateExtra-methods

Additional annotations for ExomeDepth objects

ExomeCount

Example dataset for ExomeDepth

getBamCounts

Get count data for multiple exomes

select.reference.set

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

get.power.betabinom

Estimate the power to compare two beta-binomial distributions.

show-methods

~~ Methods for Function show ~~

Conrad.hg19.common.CNVs

Conrad et al common CNVs

ExomeDepth-class

Class ExomeDepth

qbetabinom.ab

Quantile function for the beta-binomial distribution

AnnotateExtra

Add annotations to a ExomeDepth object

CallCNVs

Call CNV data from an ExomeDepth object.

countBamInGRanges.exomeDepth

Compute read count data from BAM files.

somatic.CNV.call

Call somatic variants between healthy and disease tissues.

plot-methods

~~ Methods for Function plot ~~

viterbi.hmm

Computes the Viterbi path for a hidden markov model

qbetabinom

Quantile for betabin function

TestCNV

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

ExomeDepth-package

Read depth based CNV calls for exome DNA sequence data

initialize-methods

~~ Methods for Function initialize ~~

exons.hg19.X

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

exons.hg19

Positions of exons on build hg19 of the human genome