getEnrichmentTable-GreatJob-method.RdGet a single enrichment table from GREAT web server
# S4 method for GreatJob
getEnrichmentTable(object, ontology, ...)A GreatJob-class object returned by submitGreatJob.
A single ontology names. Valid values are in availableOntologies.
All pass to getEnrichmentTables,GreatJob-method.
A data frame of the enrichment results for a single ontology.
job = readRDS(system.file("extdata", "GreatJob.rds", package = "rGREAT"))
tb = getEnrichmentTable(job, ontology = "GO Molecular Function")
#> The default enrichment table does not contain informatin of associated
#> genes for each input region. You can set `download_by = 'tsv'` to
#> download the complete table, but note only the top 500 regions can be
#> retreived. See the following link:
#>
#> https://great-help.atlassian.net/wiki/spaces/GREAT/pages/655401/Export#Export-GlobalExport
#>
#> Except the additional gene-region association column if taking 'tsv' as
#> the source of result, all other columns are the same if you choose
#> 'json' (the default) as the source. Or you can try the local GREAT
#> analysis with the function `great()`.
head(tb)
#> ID
#> 1 GO:0070696
#> 2 GO:0033612
#> 3 GO:0070700
#> 4 GO:0039706
#> 5 GO:0043997
#> 6 GO:0016628
#> name
#> 1 transmembrane receptor protein serine/threonine kinase binding
#> 2 receptor serine/threonine kinase binding
#> 3 BMP receptor binding
#> 4 co-receptor binding
#> 5 histone acetyltransferase activity (H4-K12 specific)
#> 6 oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
#> Binom_Genome_Fraction Binom_Expected Binom_Observed_Region_Hits
#> 1 3.455733e-03 3.455733000 11
#> 2 3.596413e-03 3.596413000 11
#> 3 2.138904e-03 2.138904000 8
#> 4 2.267472e-03 2.267472000 8
#> 5 3.014312e-06 0.003014312 1
#> 6 2.076881e-03 2.076881000 7
#> Binom_Fold_Enrichment Binom_Region_Set_Coverage Binom_Raw_PValue
#> 1 3.183116 0.011 0.0008981541
#> 2 3.058603 0.011 0.0012301660
#> 3 3.740233 0.008 0.0016393810
#> 4 3.528158 0.008 0.0023418690
#> 5 331.750600 0.001 0.0030097780
#> 6 3.370439 0.007 0.0054752450
#> Binom_Adjp_BH Hyper_Total_Genes Hyper_Expected Hyper_Observed_Gene_Hits
#> 1 1 13 0.99380020 5
#> 2 1 15 1.14669300 5
#> 3 1 9 0.68801550 4
#> 4 1 10 0.76446170 4
#> 5 1 1 0.07644617 1
#> 6 1 24 1.83470800 5
#> Hyper_Fold_Enrichment Hyper_Gene_Set_Coverage Hyper_Term_Gene_Coverage
#> 1 5.031192 0.0035260930 0.3846154
#> 2 4.360367 0.0035260930 0.3333333
#> 3 5.813822 0.0028208740 0.4444444
#> 4 5.232440 0.0028208740 0.4000000
#> 5 13.081100 0.0007052186 1.0000000
#> 6 2.725229 0.0035260930 0.2083333
#> Hyper_Raw_PValue Hyper_Adjp_BH
#> 1 0.001982437 0.4919942
#> 2 0.004066220 0.6862153
#> 3 0.003134656 0.6297673
#> 4 0.004910112 0.7832638
#> 5 0.076446170 1.0000000
#> 6 0.032459480 1.0000000