GREAT Analysis - Functional Enrichment on Genomic Regions


[Up] [Top]

Documentation for package ‘rGREAT’ version 2.8.0

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 GO gene sets from BioMart
getGeneSetsFromOrgDb Get GO gene sets from OrgDb object
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