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ExomeDepth (version 0.9.7)
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
0.9.7
License
GPL-3
Maintainer
Vincent Plagnol
Last Published
December 11th, 2012
Functions in ExomeDepth (0.9.7)
Search functions
exons.hg19.X
Positions of exons on build hg19 of the human genome and on chromosome X
AnnotateExtra-methods
Additional annotations for ExomeDepth objects
get.power.betabinom
Estimate the power to compare two beta-binomial distributions.
TestCNV
Computes the Bayes Factor in favour of a CNV defined by position and type.
plot-methods
~~ Methods for Function
plot
~~
qbetabinom
Quantile for betabin function
ExomeDepth-class
Class
ExomeDepth
ExomeCount
Example dataset for ExomeDepth
viterbi.hmm
Computes the Viterbi path for a hidden markov model
countBamInGRanges.exomeDepth
Compute read count data from BAM files.
somatic.CNV.call
Call somatic variants between healthy and disease tissues.
CallCNVs
Call CNV data from an ExomeDepth object.
Conrad.hg19.common.CNVs
Conrad et al common CNVs
exons.hg19
Positions of exons on build hg19 of the human genome
qbetabinom.ab
Quantile function for the beta-binomial distribution
ExomeDepth-package
Read depth based CNV calls for exome DNA sequence data
getBamCounts
Get count data for multiple exomes
show-methods
~~ Methods for Function
show
~~
initialize-methods
~~ Methods for Function
initialize
~~
AnnotateExtra
Add annotations to a ExomeDepth object
select.reference.set
Combine multiple samples to optimize the reference set in order to maximise the power to detect CNV.