Function reference • rGREAT

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

Reference

All functions