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.

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

View on CRAN

Functions

AddAnnotations,ExomeDepth-method Man page
AnnotateExtra Man page
AnnotateExtra,ExomeDepth-method Man page
AnnotateExtra-methods Man page
CallCNVs Man page
CallCNVs,ExomeDepth-method Man page
Conrad.hg19.common.CNVs Man page
countBam.everted Man page
countBamInGRanges.exomeDepth Man page
count.everted.reads Man page
ExomeCount Man page
ExomeDepth Man page
ExomeDepth-class Man page
ExomeDepth-package Man page
exons.hg19 Man page
exons.hg19.X Man page
genes.hg19 Man page
getBamCounts Man page
get.power.betabinom Man page
initialize,ExomeDepth-method Man page
initialize-methods Man page
plot,ANY-method Man page
plot.ExomeDepth Man page
plot,ExomeDepth,ANY-method Man page
plot,ExomeDepth-method Man page
plot-methods Man page
qbetabinom Man page
qbetabinom.ab Man page
select.reference.set Man page
show,ExomeDepth-method Man page
show-methods Man page
somatic.CNV.call Man page
TestCNV Man page
TestCNV,ExomeDepth-method Man page
viterbi.hmm Man page

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.