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

## Documentation for package ‘refGenome’ version 1.7.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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"'