# GREAT Analysis - Functional Enrichment on Genomic Regions

## Documentation for package ‘rGREAT’ version 2.2.0

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

## Help Pages

availableCategories | Available ontology categories of the GREAT job
availableCategories-method | Available ontology categories of the GREAT job
availableOntologies | All available ontology names of the GREAT job
availableOntologies-method | All available ontology names of the GREAT job
extendTSS | Extend TSS
extendTSSFromDataFrame | Extend TSS
extendTSSFromOrgDb | Extend TSS
extendTSSFromTxDb | Extend TSS
getEnrichmentTable | Method dispatch page for getEnrichmentTable
getEnrichmentTable-method | Get a single enrichment table from GREAT web server
getEnrichmentTable-method | Get enrichment table
getEnrichmentTables | Method dispatch page for getEnrichmentTables
getEnrichmentTables-method | Get enrichment tables from GREAT web server
getEnrichmentTables-method | Get enrichment table
getGapFromUCSC | Get gap regions from UCSC
getGeneSetsFromBioMart | Get gene sets from BioMart
getGenesFromGencode | Get Gencode genes
getGenomeDataFromNCBI | Get genome data from NCBI
getGREATDefaultTSS | Get built-in TSS from GREAT
getKEGGGenome | Get the corresponding assembly id for a kegg organism
getKEGGPathways | Get KEGG pathway gene sets
getRefSeqGenesFromUCSC | Get RefSeq genes from UCSC
getRegionGeneAssociations | Method dispatch page for getRegionGeneAssociations
getRegionGeneAssociations-method | Get region-gene associations
getRegionGeneAssociations-method | Get region-gene associations
getTSS | Get the internally used TSS
great | Perform GREAT analysis
GreatJob | Constructor method for GreatJob class
GreatJob-class | Class to store and retrieve GREAT results
GreatObject | Constructor method for GreatObject class
GreatObject-class | Class for local GREAT analysis
great_opt | Global parameters for rGREAT
plotRegionGeneAssociationGraphs | Plot region-gene associations
plotRegionGeneAssociationGraphs-method | Plot region-gene associations
plotRegionGeneAssociations | Method dispatch page for plotRegionGeneAssociations
plotRegionGeneAssociations-method | Plot region-gene associations
plotRegionGeneAssociations-method | Plot region-gene associations
plotVolcano | Method dispatch page for plotVolcano
plotVolcano-method | Make volcano plot
plotVolcano-method | Make volcano plot
randomRegions | Generate random regions
randomRegionsFromBioMartGenome | Generate random regions from a BioMart genome
read_gmt | Read gmt gene sets file
reduce_by_start_and_end | Reduce by start and end
shinyReport | Method dispatch page for shinyReport
shinyReport-method | Shiny app on the GreatJob object
shinyReport-method | Shiny app on the GreatObject object
submitGreatJob | Perform online GREAT analysis