RDocumentation
Moon
Learn R
Search all packages and functions
⚠️
There's a newer version (1.1.16) of this package.
Take me there.
ExomeDepth (version 0.9.8)
Calls CNV from exome sequence data
Description
Calls copy number variants (CNVs) from targeted sequence data
Copy Link
Copy
Link to current version
Version
Version
1.1.16
1.1.15
1.1.12
1.1.10
1.1.8
1.1.6
1.1.5
1.1.4
1.1.1
1.0.7
1.0.5
1.0.0
0.9.8
0.9.7
0.9.4
0.9.2
0.9.1
0.8.4
0.8.3
0.8.0
0.7.3
0.6.3
Down Chevron
Install
install.packages('ExomeDepth')
Monthly Downloads
115
Version
0.9.8
License
GPL-3
Maintainer
Vincent Plagnol
Last Published
December 11th, 2013
Functions in ExomeDepth (0.9.8)
Search functions
AnnotateExtra-methods
Additional annotations for ExomeDepth objects
ExomeCount
Example dataset for ExomeDepth
getBamCounts
Get count data for multiple exomes
select.reference.set
Combine multiple samples to optimize the reference set in order to maximise the power to detect CNV.
get.power.betabinom
Estimate the power to compare two beta-binomial distributions.
show-methods
~~ Methods for Function
show
~~
Conrad.hg19.common.CNVs
Conrad et al common CNVs
ExomeDepth-class
Class
ExomeDepth
qbetabinom.ab
Quantile function for the beta-binomial distribution
AnnotateExtra
Add annotations to a ExomeDepth object
CallCNVs
Call CNV data from an ExomeDepth object.
countBamInGRanges.exomeDepth
Compute read count data from BAM files.
somatic.CNV.call
Call somatic variants between healthy and disease tissues.
plot-methods
~~ Methods for Function
plot
~~
viterbi.hmm
Computes the Viterbi path for a hidden markov model
qbetabinom
Quantile for betabin function
TestCNV
Computes the Bayes Factor in favour of a CNV defined by position and type.
ExomeDepth-package
Read depth based CNV calls for exome DNA sequence data
initialize-methods
~~ Methods for Function
initialize
~~
exons.hg19.X
Positions of exons on build hg19 of the human genome and on chromosome X
exons.hg19
Positions of exons on build hg19 of the human genome