ISAKEGG (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. KEGGListHyperGResult
object. The hypergeometric test, a version Fisher's exact test, takes a KEGG
pathway and a gene set (in our case coming from an ISA module) and asks
whether the number of genes in the set participating in the pathway, is
significantly more (or less) than what one would expect by chance.
ISAKEGG
performs the hypergeometric test for every module, for
all KEGG pathways. The KEGG data is taken from the KEGG.db
package and the annotation package of the chip.
ISAKEGG
currently cannot test for under-representation.
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M., The KEGG resource for deciphering the genome, Nucleic Acids Res. 2004 Jan 1;32(Database issue):D277-80. Bergmann S, Ihmels J, Barkai N: Iterative signature algorithm for the analysis of large-scale gene expression data Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):031902. Epub 2003 Mar 11.
ISAGO
, ISACHR
,
ISAmiRNA
for other enrichment calculations. The KEGG.db
and Category
packages.
data(ALLModulesSmall)
KEGG <- ISAKEGG(ALLModulesSmall)
KEGG
sigCategories(KEGG)[[1]]
summary(KEGG)[[1]][,1:5]
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