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ExomeDepth (version 0.7.3)
Calls CNV from exome sequence data
Description
Calls copy number variants (CNVs) from targeted sequence data
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Install
install.packages('ExomeDepth')
Monthly Downloads
115
Version
0.7.3
License
GPL-3
Maintainer
Vincent Plagnol
Last Published
February 23rd, 2012
Functions in ExomeDepth (0.7.3)
Search functions
exons.hg19
Positions of exons on build hg19 of the human genome
qbetabinom.ab
Quantile function for the beta-binomial distribution
get.power.betabinom
Estimate the power to compare two beta-binomial distributions.
ExomeDepth-package
Read depth based CNV calls for exome DNA sequence data
ExomeDepth-class
Class
ExomeDepth
TestCNV
Computes the Bayes Factor in favour of a CNV defined by position and type.
viterbi.hmm
Computes the Viterbi path for a hidden markov model
ExomeCount
Example dataset for ExomeDepth
countBamInGRanges.exomeDepth
Compute read count data from BAM files.
qbetabinom
Quantile for betabin function
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
CallCNVs
Call CNV data from an ExomeDepth object.