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ExomeDepth (version 0.6.3)

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

0.6.3

License

GPL-3

Maintainer

Vincent Plagnol

Last Published

February 1st, 2012

Functions in ExomeDepth (0.6.3)

AddAnnotations

Add annotation data to an exome dataset (i.e. position and names of the exons)
exons.hg19

Positions of exons on build hg19 of the human genome
ExomeDepth-package

Read depth based CNV calls for exome DNA sequence data
viterbi.hmm

Computes the Viterbi path for a hidden markov model
qbetabinom

Quantile for betabin function
get.power.betabinom

Estimate the power to compare two beta-binomial distributions.
ExomeCount

Example dataset for ExomeDepth
ExomeDepth-class

Class ExomeDepth
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
CallCNVs

Call CNV data from an ExomeDepth object.
TestCNV

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

Get count data for multiple exomes
countBamInGRanges.exomeDepth

Compute read count data from BAM files.