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


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Documentation for package ‘refGenome’ version 1.7.3

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

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 --

geneId<- Class '"geneModel"'
geneId<--method Class '"geneModel"'
geneId<--methods Class '"geneModel"'
geneList Class '"geneList"'
geneList-class Class '"geneList"'
geneList-method Class '"geneList"'
geneList-methods Class '"geneList"'
geneModel Class '"geneModel"'
geneModel-class Class '"geneModel"'
geneModel-method Class '"geneModel"'
geneModel-methods Class '"geneModel"'
geneName<- Class '"geneModel"'
geneName<--method Class '"geneModel"'
geneName<--methods Class '"geneModel"'
getCdsData Class '"transcriptModel"'
getCdsData-method Class '"transcriptModel"'
getCdsData-methods Class '"transcriptModel"'
getExonData Class '"transcriptModel"'
getExonData-method Class '"transcriptModel"'
getExonData-methods Class '"transcriptModel"'
getGeneId Extract gene ID from gene-name and getGeneId.
getGeneId-method Extract gene ID from gene-name and getGeneId.
getGeneId-methods Extract gene ID from gene-name and getGeneId.
getGenePositions Extract subsets of refGenome by gene-name.
getGenePositions-method Extract subsets of refGenome by gene-name.
getGenePositions-method Class '"ucscGenome"'
getGenePositions-methods Extract subsets of refGenome by gene-name.
getGeneTable Class '"ensemblGenome"'
getGeneTable-method Class '"ensemblGenome"'
getGeneTable-method Class '"ucscGenome"'
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"'
getTranscript Class '"transcriptModel"'
getTranscript-method Class '"transcriptModel"'
getTranscript-methods Class '"transcriptModel"'
getXref Class '"ucscGenome"'
getXref-method Class '"ucscGenome"'
getXref-methods Class '"ucscGenome"'

-- I --

initialize-method Class '"geneList"'
initialize-method Class '"geneModel"'
initialize-method Class '"refGenome"'
initialize-method Class '"transcriptModel"'

-- L --

length-method Class '"geneList"'
loadGenome Saving and loading 'refGenome' objects
loadGenomeDb Saving and loading 'refGenome' objects to and from SQLite databases.

-- N --

names-method Class '"geneList"'
names<--method Class '"geneList"'

-- O --

overlap overlap function
overlapJuncs overlapJuncs function

-- P --

plot.geneModel Class '"geneModel"'
plot.transcriptModel Class '"transcriptModel"'
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"'
show-method Class '"geneList"'

-- 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"'
transcriptModel-class Class '"transcriptModel"'

-- 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.

-- misc --

+-method Class '"geneList"'
+-method Class '"geneModel"'
[-method Class '"geneList"'