Retrieving Annotation data from runTest() created object
For differential expression rna-seq analysis using gene ontology, following command was used to get topGOresults as
topGOresults <- runTest(topGOobject, algorithm = "weight01", statistic = "fisher")
topGOresults
and i got the output as follows
Description:
Ontology: MF
'weight01' algorithm with the 'fisher' test
37 GO terms scored: 6 terms with p < 0.01
Annotation data:
Annotated genes: 18978
Significant genes: 3441
Min. no. of genes annotated to a GO: 10
Nontrivial nodes: 37
where is this annotation data stored and how can it be retrieved? Is there any way i can extract number of nontrivial nodes automatically without checking for the result?
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Sreeraj Thamban
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