ISAGO (modules, ann = annotation(modules), features = featureNames(modules), hgCutoff = 0.05, correction = TRUE, correction.method = "holm")
ISAModules
object, a set of ISA modules.modules
argument.modules
argument.p.adjust
function for details on these. GOListHyperGResult
objects, for
the three Gene Ontologies, named
The Gene Ontology database has three big sub-graphs, the root nodes (the most general terms) of these are the direct children of the root term of the whole ontology: biological process, cellular component, molecular function. They are usually referred to as ontologies.
The hypergeometric test, a version Fisher's exact test, takes a GO
term and a gene set (in our case coming from an ISA module) and asks
whether the number of genes in the set annotated by the term is
significantly more (or less) than what one would expect by chance.
ISAGO
performs the hypergeometric test for every module, for
all GO terms of the three GO ontologies. The GO data is taken from the
GO.db
package and the annotation package of the chip.
ISAGO
currently cannot test for under-representation and the
conditional test, as implemented in the GOstats
package, is not
available either.
ISAKEGG
, ISACHR
,
ISAmiRNA
for other enrichment calculations. The GO.db
, GOstats
and Category
packages.
data(ALLModulesSmall)
GO <- ISAGO(ALLModulesSmall)
GO
summary(GO$BP)[[1]][,1:5]
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