Gene and Splice Site Annotation Using Annotation Data from Ensembl and UCSC Genome Browsers


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Documentation for package ‘refGenome’ version 1.6.0

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A B E G I L O P R S T U W

refGenome-package Managing annotation data for reference Genomes from UCSC and Ensembl.

-- A --

addEnsembl Class '"ucscGenome"'
addEnsembl-method Class '"ucscGenome"'
addEnsembl-methods Class '"ucscGenome"'
addIsCoding Add information on coding/non-coding status.
addIsCoding-method Add information on coding/non-coding status.
addIsCoding-methods Add information on coding/non-coding status.
addIsoforms Class '"ucscGenome"'
addIsoforms-method Class '"ucscGenome"'
addIsoforms-methods Class '"ucscGenome"'
addXref Class '"ucscGenome"'
addXref-method Class '"ucscGenome"'
addXref-methods Class '"ucscGenome"'

-- B --

basedir Class '"refGenome"'
basedir-method Class '"refGenome"'
basedir-methods Class '"refGenome"'
basedir<- Class '"refGenome"'
basedir<--method Class '"refGenome"'
basedir<--methods Class '"refGenome"'

-- E --

ensemblExons Class '"refExons"'
ensemblExons-class Class '"refExons"'
ensemblGenome Class '"ensemblGenome"'
ensemblGenome-class Class '"ensemblGenome"'
ensemblJunctions Class '"refJunctions"'
ensemblJunctions-class Class '"refJunctions"'
ensPrimAssembly Class '"refGenome"'
extractByGeneId Extract subsets of refGenome by gene-ID.
extractByGeneId-method Extract subsets of refGenome by gene-ID.
extractByGeneId-methods Extract subsets of refGenome by gene-ID.
extractByGeneName Extract subsets of refGenome by gene-name.
extractByGeneName-method Extract subsets of refGenome by gene-name.
extractByGeneName-methods Extract subsets of refGenome by gene-name.
extractFeature Class '"refGenome"'
extractFeature-method Class '"refGenome"'
extractFeature-methods Class '"refGenome"'
extractPaGenes Class '"ensemblGenome"'
extractPaGenes-method Class '"ensemblGenome"'
extractPaGenes-methods Class '"ensemblGenome"'
extractSeqids Class '"refGenome"'
extractSeqids-method Class '"refGenome"'
extractSeqids-methods Class '"refGenome"'
extractTranscript Class '"refGenome"'
extractTranscript-method Class '"refGenome"'
extractTranscript-method Class '"ucscGenome"'
extractTranscript-methods Class '"refGenome"'

-- G --

getGenePositions Extract subsets of refGenome by gene-name.
getGenePositions-method Extract subsets of refGenome by gene-name.
getGenePositions-methods Extract subsets of refGenome by gene-name.
getGeneTable Class '"ensemblGenome"'
getGeneTable-method Class '"ensemblGenome"'
getGeneTable-methods Class '"ensemblGenome"'
getGtf Class '"refGenome"'
getGtf-method Class '"refGenome"'
getGtf-methods Class '"refGenome"'
getSpliceTable Class '"refJunctions"'
getSpliceTable-method Class '"refJunctions"'
getSpliceTable-methods Class '"refJunctions"'
getXref Class '"ucscGenome"'
getXref-method Class '"ucscGenome"'
getXref-methods Class '"ucscGenome"'

-- I --

initialize-method Class '"refGenome"'

-- L --

loadGenome Saving and loading 'refGenome' objects
loadGenomeDb Saving and loading 'refGenome' objects to and from SQLite databases.

-- O --

overlap overlap function
overlapJuncs overlapJuncs function

-- P --

plotUbs Unification of Exonic ranges.
plotUbs-method Unification of Exonic ranges.
plotUbs-methods Unification of Exonic ranges.

-- R --

read.gtf Reading and parsing GTF files into refGenome objects.
read.gtf-method Reading and parsing GTF files into refGenome objects.
read.gtf-methods Reading and parsing GTF files into refGenome objects.
refExons Class '"refExons"'
refExons-class Class '"refExons"'
refExons-method Class '"refExons"'
refExons-methods Class '"refExons"'
refGenome-class Class '"refGenome"'
refJunctions Class '"refJunctions"'
refJunctions-class Class '"refJunctions"'

-- S --

saveGenome Saving and loading 'refGenome' objects
saveGenome-method Saving and loading 'refGenome' objects
saveGenome-methods Saving and loading 'refGenome' objects
setGtf Class '"refGenome"'
setGtf-method Class '"refGenome"'
setGtf-methods Class '"refGenome"'

-- T --

tableFeatures Class '"ensemblGenome"'
tableFeatures-method Class '"ensemblGenome"'
tableFeatures-method Class '"ucscGenome"'
tableFeatures-methods Class '"ensemblGenome"'
tableSeqids Class '"refGenome"'
tableSeqids-method Class '"refGenome"'
tableSeqids-methods Class '"refGenome"'
tableTranscript.id Class '"ensemblGenome"'
tableTranscript.id-method Class '"ensemblGenome"'
tableTranscript.id-method Class '"ucscGenome"'
tableTranscript.id-methods Class '"ensemblGenome"'
tableTranscript.name Class '"ensemblGenome"'
tableTranscript.name-method Class '"ensemblGenome"'
tableTranscript.name-methods Class '"ensemblGenome"'

-- U --

ucPrimAssembly Class '"refGenome"'
ucscExons Class '"refExons"'
ucscExons-class Class '"refExons"'
ucscGenome Class '"ucscGenome"'
ucscGenome-class Class '"ucscGenome"'
ucscJunctions Class '"refJunctions"'
ucscJunctions-class Class '"refJunctions"'
unifiedExons-class Class '"refExons"'
unifyJuncs Unification of splice-junctions.
unifyJuncs-method Unification of splice-junctions.
unifyJuncs-methods Unification of splice-junctions.
unifyRanges Unification of Exonic ranges.
unifyRanges-method Unification of Exonic ranges.
unifyRanges-methods Unification of Exonic ranges.

-- W --

writeDB Saving and loading 'refGenome' objects to and from SQLite databases.
writeDB-method Saving and loading 'refGenome' objects to and from SQLite databases.
writeDB-methods Saving and loading 'refGenome' objects to and from SQLite databases.