ExomeDepth: Calls Copy Number Variants from Targeted Sequence Data
Version 1.1.10

Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.

AuthorVincent Plagnol
Date of publication2016-05-15 09:48:08
MaintainerVincent Plagnol <v.plagnol@ucl.ac.uk>
LicenseGPL-3
Version1.1.10
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ExomeDepth")

Getting started

Package overview

Popular man pages

countBamInGRanges.exomeDepth: Compute read count data from BAM files.
exons.hg19: Positions of exons on build hg19 of the human genome
getBamCounts: Get count data for multiple exomes
initialize-methods: ~~ Methods for Function 'initialize' ~~
plot.ExomeDepth: Plotting function for ExomeDepth objects
qbetabinom.ab: Quantile function for the beta-binomial distribution
select.reference.set: Combine multiple samples to optimize the reference set in...
See all...

All man pages Function index File listing

Man pages

AnnotateExtra: Add annotations to a ExomeDepth object
AnnotateExtra-methods: Additional annotations for ExomeDepth objects
CallCNVs: Call CNV data from an ExomeDepth object.
Conrad.hg19.common.CNVs: Conrad et al common CNVs
countBam.everted: Counts everted reads from a single BAM file
countBamInGRanges.exomeDepth: Compute read count data from BAM files.
count.everted.reads: Count the number of everted reads for a set of BAM files.
ExomeCount: Example dataset for ExomeDepth
ExomeDepth-class: Class 'ExomeDepth'
ExomeDepth-package: Read depth based CNV calls for exome DNA sequence data
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...
genes.hg19: Positions of genes on build hg19 of the human genome
getBamCounts: Get count data for multiple exomes
get.power.betabinom: Estimate the power to compare two beta-binomial...
initialize-methods: ~~ Methods for Function 'initialize' ~~
plot.ExomeDepth: Plotting function for ExomeDepth objects
qbetabinom: Quantile for betabin function
qbetabinom.ab: Quantile function for the beta-binomial distribution
select.reference.set: Combine multiple samples to optimize the reference set in...
show-methods: ~~ Methods for Function 'show' ~~
somatic.CNV.call: Call somatic variants between healthy and disease tissues.
TestCNV: Computes the Bayes Factor in favour of a CNV defined by...
viterbi.hmm: Computes the Viterbi path for a hidden markov model

Functions

Files

inst
inst/doc
inst/doc/ExomeDepth-vignette.R
inst/doc/ExomeDepth-vignette.Rnw
inst/doc/ExomeDepth-vignette.pdf
src
src/VP_gamma.c
src/invhyp.c
src/chebyshev.h
src/gsl_math.h
src/gsl_nan.h
src/hmm.cpp
src/gsl_sf_trig.h
src/gsl_sf_log.h
src/VP_zeta.c
src/gsl_message.h
src/gsl_complex.h
src/log1p.c
src/VP_infnan.c
src/gsl_sf_gamma.h
src/gsl_inline.h
src/error.h
src/gsl_sf_exp.h
src/gsl_sf_psi.h
src/hypot.c
src/CNV_estimate.cpp
src/beta.c
src/fdiv.c
src/gsl_precision.h
src/config.h
src/error.c
src/check.h
src/math.c
src/gsl_pow_int.h
src/gsl_sf_elementary.h
src/gsl_types.h
src/VP_trig.c
src/exp.c
src/eval.h
src/VP_psi.c
src/gsl_sf_zeta.h
src/stream.c
src/gsl_complex_math.h
src/gsl_sf_pow_int.h
src/gsl_sf_result.h
src/gsl_errno.h
src/gsl_sys.h
src/ldfrexp.c
src/gsl_machine.h
src/VP_log.c
src/elementary.c
NAMESPACE
data
data/genes.hg19.RData
data/Conrad.hg19.RData
data/exons.hg19.RData
data/datalist
data/exons.hg19.X.RData
data/ExomeCount.RData
R
R/plot_CNVs_method.R
R/tools.R
R/class_definition.R
R/countBamInGranges.R
R/zzz.R
R/optimize_reference_set.R
vignettes
vignettes/.install_extras
vignettes/ExomeDepth-vignette.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/exons.hg19.X.Rd
man/plot.ExomeDepth.Rd
man/countBamInGRanges.exomeDepth.Rd
man/AnnotateExtra-methods.Rd
man/somatic.CNV.call.Rd
man/count.everted.reads.Rd
man/exons.hg19.Rd
man/getBamCounts.Rd
man/initialize-methods.Rd
man/CallCNVs.Rd
man/ExomeDepth-class.Rd
man/ExomeDepth-package.Rd
man/AnnotateExtra.Rd
man/Conrad.hg19.common.CNVs.Rd
man/ExomeCount.Rd
man/viterbi.hmm.Rd
man/qbetabinom.Rd
man/get.power.betabinom.Rd
man/select.reference.set.Rd
man/qbetabinom.ab.Rd
man/genes.hg19.Rd
man/countBam.everted.Rd
man/TestCNV.Rd
man/show-methods.Rd
ExomeDepth documentation built on May 19, 2017, 10:28 a.m.

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