ExomeDepth: Calls Copy Number Variants from Targeted Sequence Data

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

Author
Vincent Plagnol
Date of publication
2016-05-15 09:48:08
Maintainer
Vincent Plagnol <v.plagnol@ucl.ac.uk>
License
GPL-3
Version
1.1.10

View on CRAN

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

Files in this package

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