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ExomeDepth (version 1.0.7)
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
1.0.7
License
GPL-3
Maintainer
Vincent Plagnol
Last Published
July 20th, 2014
Functions in ExomeDepth (1.0.7)
Search functions
get.power.betabinom
Estimate the power to compare two beta-binomial distributions.
count.everted.reads
Count the number of everted reads for a set of BAM files.
qbetabinom.ab
Quantile function for the beta-binomial distribution
ExomeDepth-class
Class
ExomeDepth
getBamCounts
Get count data for multiple exomes
show-methods
~~ Methods for Function
show
~~
plot-methods
~~ Methods for Function
plot
~~
exons.hg19.X
Positions of exons on build hg19 of the human genome and on chromosome X
ExomeCount
Example dataset for ExomeDepth
TestCNV
Computes the Bayes Factor in favour of a CNV defined by position and type.
CallCNVs
Call CNV data from an ExomeDepth object.
viterbi.hmm
Computes the Viterbi path for a hidden markov model
ExomeDepth-package
Read depth based CNV calls for exome DNA sequence data
qbetabinom
Quantile for betabin function
countBamInGRanges.exomeDepth
Compute read count data from BAM files.
Conrad.hg19.common.CNVs
Conrad et al common CNVs
AnnotateExtra-methods
Additional annotations for ExomeDepth objects
initialize-methods
~~ Methods for Function
initialize
~~
exons.hg19
Positions of exons on build hg19 of the human genome
countBam.everted
Counts everted reads from a single BAM file
genes.hg19
Positions of genes on build hg19 of the human genome
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.
somatic.CNV.call
Call somatic variants between healthy and disease tissues.