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ExomeDepth (version 0.8.0)
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
0.8.0
License
GPL-3
Maintainer
Vincent Plagnol
Last Published
April 28th, 2012
Functions in ExomeDepth (0.8.0)
Search functions
qbetabinom
Quantile for betabin function
getBamCounts
Get count data for multiple exomes
ExomeDepth-package
Read depth based CNV calls for exome DNA sequence data
TestCNV
Computes the Bayes Factor in favour of a CNV defined by position and type.
get.power.betabinom
Estimate the power to compare two beta-binomial distributions.
CallCNVs
Call CNV data from an ExomeDepth object.
ExomeCount
Example dataset for ExomeDepth
qbetabinom.ab
Quantile function for the beta-binomial distribution
exons.hg19
Positions of exons on build hg19 of the human genome
plot-methods
~~ Methods for Function
plot
~~
viterbi.hmm
Computes the Viterbi path for a hidden markov model
ExomeDepth-class
Class
ExomeDepth
countBamInGRanges.exomeDepth
Compute read count data from BAM files.
select.reference.set
Combine multiple samples to optimize the reference set in order to maximise the power to detect CNV.