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ExomeDepth (version 0.9.1)
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
0.9.1
License
GPL-3
Maintainer
Vincent Plagnol
Last Published
October 19th, 2012
Functions in ExomeDepth (0.9.1)
Search functions
Conrad.hg19.common.CNVs
Conrad et al common CNVs
getBamCounts
Get count data for multiple exomes
viterbi.hmm
Computes the Viterbi path for a hidden markov model
initialize-methods
~~ Methods for Function
initialize
~~
AnnotateExtra
Add annotations to a ExomeDepth object
qbetabinom
Quantile for betabin function
plot-methods
~~ Methods for Function
plot
~~
CallCNVs
Call CNV data from an ExomeDepth object.
TestCNV
Computes the Bayes Factor in favour of a CNV defined by position and type.
exons.hg19
Positions of exons on build hg19 of the human genome
countBamInGRanges.exomeDepth
Compute read count data from BAM files.
AnnotateExtra-methods
Additional annotations for ExomeDepth objects
show-methods
~~ Methods for Function
show
~~
ExomeDepth-class
Class
ExomeDepth
somatic.CNV.call
Call somatic variants between healthy and disease tissues.
select.reference.set
Combine multiple samples to optimize the reference set in order to maximise the power to detect CNV.
ExomeCount
Example dataset for ExomeDepth
exons.hg19.X
Positions of exons on build hg19 of the human genome and on chromosome X
ExomeDepth-package
Read depth based CNV calls for exome DNA sequence data
qbetabinom.ab
Quantile function for the beta-binomial distribution
get.power.betabinom
Estimate the power to compare two beta-binomial distributions.