ISAmiRNA (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. miRNAListHyperGResult
object.TargetScan is a database of predicted miRNA targets. The predictions are done based many factors, including the conservation of the target region during evolution.
The hypergeometric test, a version Fisher's exact test, takes a miRNA
and a gene set (in our case coming from an ISA module) and asks
whether the number of genes in the set regulated by the miRNA is
significantly more (or less) than what one would expect by chance.
ISAmiRNA
performs the hypergeometric test for every module,
for all miRNAs in the TargetScan database.
In order to use this function, TargetScan annotation packages are needed.
ISAGO
, ISAKEGG
and
ISACHR
for other enrichment calculations. The Category
package.
data(ALLModulesSmall)
if (require(targetscan.Hs.eg.db)) {
miRNA <- ISAmiRNA(ALLModulesSmall)
summary(miRNA, p=0.1)[[7]]
}
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