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ExomeDepth (version 1.0.0)
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
117
Version
1.0.0
License
GPL-3
Maintainer
Vincent Plagnol
Last Published
February 12th, 2014
Functions in ExomeDepth (1.0.0)
Search functions
ExomeCount
Example dataset for ExomeDepth
plot-methods
~~ Methods for Function
plot
~~
somatic.CNV.call
Call somatic variants between healthy and disease tissues.
TestCNV
Computes the Bayes Factor in favour of a CNV defined by position and type.
CallCNVs
Call CNV data from an ExomeDepth object.
Conrad.hg19.common.CNVs
Conrad et al common CNVs
count.everted.reads
Count the number of everted reads for a set of BAM files.
countBamInGRanges.exomeDepth
Compute read count data from BAM files.
ExomeDepth-class
Class
ExomeDepth
initialize-methods
~~ Methods for Function
initialize
~~
ExomeDepth-package
Read depth based CNV calls for exome DNA sequence data
show-methods
~~ Methods for Function
show
~~
countBam.everted
Counts everted reads from a single BAM file
viterbi.hmm
Computes the Viterbi path for a hidden markov model
exons.hg19
Positions of exons on build hg19 of the human genome
exons.hg19.X
Positions of exons on build hg19 of the human genome and on chromosome X
AnnotateExtra-methods
Additional annotations for ExomeDepth objects
qbetabinom
Quantile for betabin function
AnnotateExtra
Add annotations to a ExomeDepth object
getBamCounts
Get count data for multiple exomes
get.power.betabinom
Estimate the power to compare two beta-binomial distributions.
qbetabinom.ab
Quantile function for the beta-binomial distribution
genes.hg19
Positions of genes on build hg19 of the human genome
select.reference.set
Combine multiple samples to optimize the reference set in order to maximise the power to detect CNV.