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ExomeDepth (version 0.9.4)
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
0.9.4
License
GPL-3
Maintainer
Vincent Plagnol
Last Published
October 24th, 2012
Functions in ExomeDepth (0.9.4)
Search functions
ExomeDepth-package
Read depth based CNV calls for exome DNA sequence data
AnnotateExtra-methods
Additional annotations for ExomeDepth objects
plot-methods
~~ Methods for Function
plot
~~
AnnotateExtra
Add annotations to a ExomeDepth object
get.power.betabinom
Estimate the power to compare two beta-binomial distributions.
Conrad.hg19.common.CNVs
Conrad et al common CNVs
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
ExomeDepth-class
Class
ExomeDepth
somatic.CNV.call
Call somatic variants between healthy and disease tissues.
initialize-methods
~~ Methods for Function
initialize
~~
qbetabinom
Quantile for betabin function
show-methods
~~ Methods for Function
show
~~
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
exons.hg19.X
Positions of exons on build hg19 of the human genome and on chromosome X
ExomeCount
Example dataset for ExomeDepth
CallCNVs
Call CNV data from an ExomeDepth object.
countBamInGRanges.exomeDepth
Compute read count data from BAM files.
getBamCounts
Get count data for multiple exomes
exons.hg19
Positions of exons on build hg19 of the human genome