GeneBreak: Gene Break Detection
Version 1.6.0

Recurrent breakpoint gene detection on copy number aberration profiles.

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AuthorEvert van den Broek, Stef van Lieshout
Bioconductor views CopyNumberVariation DNASeq Genetics Sequencing Visualization WholeGenome aCGH
Date of publicationNone
MaintainerEvert van den Broek <vandenbroek.evert@gmail.com>
LicenseGPL-2
Version1.6.0
URL https://github.com/stefvanlieshout/GeneBreak
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GeneBreak")

Man pages

accessOptions-CopyNumberBreakPoints-method: Access Object Data. This method lists possible functions to...
addGeneAnnotation-CopyNumberBreakPoints-method: addGeneAnnotation
bpFilter-CopyNumberBreakPoints-method: bpFilter
bpGenes-CopyNumberBreakPointGenes-method: bpGenes
bpPlot-CopyNumberBreakPoints-method: bpPlot
bpStats-CopyNumberBreakPoints-method: bpStats
breakpointData-CopyNumberBreakPoints-method: Access Object breakpointData. This method returns a dataframe...
breakpointsPerGene-CopyNumberBreakPointGenes-method: Access Object breakpointsPerGene. This method returns a...
callData-CopyNumberBreakPoints-method: Access Object callData. This method returns a dataframe with...
CopyNumberBreakPointGenes-class: An S4 class to represent a CopyNumberBreakPointGenes object
CopyNumberBreakPoints-class: An S4 class to represent a CopyNumberBreakPoints object.
copynumber.data.chr18: CGHcall Example copynumber data hg18 chr18
copynumber.data.chr20: CGHcall Example copynumber data hg18 chr20
copynumber.data.chr21: CGHcall Example copynumber data hg18 chr21
ens.gene.ann.hg18: Gene Annotation hg18
ens.gene.ann.hg19: Gene Annotation hg19
ens.gene.ann.hg38: Gene Annotation hg38
featureChromosomes-CopyNumberBreakPoints-method: Access Object featureChromosomes. This method returns a...
featureInfo-CopyNumberBreakPoints-method: Access Options featureInfo. This method returns a dataframe...
featuresPerGene-CopyNumberBreakPointGenes-method: Access Object featuresPerGene. This method returns a vector...
GeneBreak: GeneBreak: A package for gene breakpoint detection on copy...
geneChromosomes-CopyNumberBreakPointGenes-method: Access Object geneChromosomes. This method returns a vector...
geneInfo-CopyNumberBreakPointGenes-method: Access Options geneInfo. This method returns a dataframe with...
getBreakpoints: getBreakpoints
namesFeatures-CopyNumberBreakPoints-method: Access Object namesFeatures. This method returns a vector...
recurrentGenes-CopyNumberBreakPointGenes-method: Access Options recurrentGenes. This method returns a...
sampleNames-CopyNumberBreakPoints-method: Access Object sampleNames. This method returns a vector with...
segmentData-CopyNumberBreakPoints-method: Access Object segmentData. This method returns a dataframe...

Functions

CopyNumberBreakPointGenes Man page
CopyNumberBreakPointGenes-class Man page
CopyNumberBreakPoints Man page
CopyNumberBreakPoints-class Man page
GeneBreak Man page
GeneBreak-package Man page
accessOptions Man page
accessOptions,CopyNumberBreakPoints-method Man page
addGeneAnnotation Man page
addGeneAnnotation,CopyNumberBreakPoints-method Man page
bpFilter Man page
bpFilter,CopyNumberBreakPoints-method Man page
bpGenes Man page
bpGenes,CopyNumberBreakPointGenes-method Man page
bpPlot Man page
bpPlot,CopyNumberBreakPoints-method Man page
bpStats Man page
bpStats,CopyNumberBreakPoints-method Man page
breakpointData Man page
breakpointData,CopyNumberBreakPoints-method Man page
breakpointsPerGene Man page
breakpointsPerGene,CopyNumberBreakPointGenes-method Man page
callData Man page
callData,CopyNumberBreakPoints-method Man page
copynumber.data.chr18 Man page
copynumber.data.chr20 Man page
copynumber.data.chr21 Man page
cumgf Source code
ens.gene.ann.hg18 Man page
ens.gene.ann.hg19 Man page
ens.gene.ann.hg38 Man page
featureChromosomes Man page
featureChromosomes,CopyNumberBreakPoints-method Man page
featureInfo Man page
featureInfo,CopyNumberBreakPoints-method Man page
featuresPerGene Man page
featuresPerGene,CopyNumberBreakPointGenes-method Man page
geneChromosomes Man page
geneChromosomes,CopyNumberBreakPointGenes-method Man page
geneInfo Man page
geneInfo,CopyNumberBreakPointGenes-method Man page
getBreakpoints Man page Source code
gilbertTest Source code
glmbreak Source code
namesFeatures Man page
namesFeatures,CopyNumberBreakPoints-method Man page
recurrentGenes Man page
recurrentGenes,CopyNumberBreakPointGenes-method Man page
runWorkflow Source code
sampleNames Man page
sampleNames,CopyNumberBreakPoints-method Man page
segmentData Man page
segmentData,CopyNumberBreakPoints-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/GeneBreakAccessors.R
R/GeneBreakMethods.R
R/dataDocumentation.R
R/pkgname.R
R/private.R
README.md
build
build/vignette.rds
data
data/copynumber.data.chr18.rda
data/copynumber.data.chr20.rda
data/copynumber.data.chr21.rda
data/datalist
data/ens.gene.ann.hg18.rda
data/ens.gene.ann.hg19.rda
data/ens.gene.ann.hg38.rda
inst
inst/doc
inst/doc/GeneBreak.R
inst/doc/GeneBreak.Rnw
inst/doc/GeneBreak.pdf
man
man/CopyNumberBreakPointGenes-class.Rd
man/CopyNumberBreakPoints-class.Rd
man/GeneBreak.Rd
man/accessOptions-CopyNumberBreakPoints-method.Rd
man/addGeneAnnotation-CopyNumberBreakPoints-method.Rd
man/bpFilter-CopyNumberBreakPoints-method.Rd
man/bpGenes-CopyNumberBreakPointGenes-method.Rd
man/bpPlot-CopyNumberBreakPoints-method.Rd
man/bpStats-CopyNumberBreakPoints-method.Rd
man/breakpointData-CopyNumberBreakPoints-method.Rd
man/breakpointsPerGene-CopyNumberBreakPointGenes-method.Rd
man/callData-CopyNumberBreakPoints-method.Rd
man/copynumber.data.chr18.Rd
man/copynumber.data.chr20.Rd
man/copynumber.data.chr21.Rd
man/ens.gene.ann.hg18.Rd
man/ens.gene.ann.hg19.Rd
man/ens.gene.ann.hg38.Rd
man/featureChromosomes-CopyNumberBreakPoints-method.Rd
man/featureInfo-CopyNumberBreakPoints-method.Rd
man/featuresPerGene-CopyNumberBreakPointGenes-method.Rd
man/geneChromosomes-CopyNumberBreakPointGenes-method.Rd
man/geneInfo-CopyNumberBreakPointGenes-method.Rd
man/getBreakpoints.Rd
man/namesFeatures-CopyNumberBreakPoints-method.Rd
man/recurrentGenes-CopyNumberBreakPointGenes-method.Rd
man/sampleNames-CopyNumberBreakPoints-method.Rd
man/segmentData-CopyNumberBreakPoints-method.Rd
vignettes
vignettes/GeneBreak.Rnw
GeneBreak documentation built on May 20, 2017, 10:36 p.m.