GREAT Analysis - Functional Enrichment on Genomic Regions


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Documentation for package ‘rGREAT’ version 2.0.0

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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
getGREATDefaultTSS Get built-in TSS from GREAT
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