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ExomeDepth (version 1.0.5)
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
105
Version
1.0.5
License
GPL-3
Maintainer
Vincent Plagnol
Last Published
June 26th, 2014
Functions in ExomeDepth (1.0.5)
Search functions
AnnotateExtra
Add annotations to a ExomeDepth object
plot-methods
~~ Methods for Function
plot
~~
exons.hg19.X
Positions of exons on build hg19 of the human genome and on chromosome X
qbetabinom
Quantile for betabin function
getBamCounts
Get count data for multiple exomes
initialize-methods
~~ Methods for Function
initialize
~~
somatic.CNV.call
Call somatic variants between healthy and disease tissues.
countBam.everted
Counts everted reads from a single BAM file
count.everted.reads
Count the number of everted reads for a set of BAM files.
ExomeCount
Example dataset for ExomeDepth
CallCNVs
Call CNV data from an ExomeDepth object.
Conrad.hg19.common.CNVs
Conrad et al common CNVs
viterbi.hmm
Computes the Viterbi path for a hidden markov model
genes.hg19
Positions of genes on build hg19 of the human genome
ExomeDepth-class
Class
ExomeDepth
AnnotateExtra-methods
Additional annotations for ExomeDepth objects
select.reference.set
Combine multiple samples to optimize the reference set in order to maximise the power to detect CNV.
ExomeDepth-package
Read depth based CNV calls for exome DNA sequence data
countBamInGRanges.exomeDepth
Compute read count data from BAM files.
exons.hg19
Positions of exons on build hg19 of the human genome
get.power.betabinom
Estimate the power to compare two beta-binomial distributions.
qbetabinom.ab
Quantile function for the beta-binomial distribution
TestCNV
Computes the Bayes Factor in favour of a CNV defined by position and type.
show-methods
~~ Methods for Function
show
~~