GOanalysis: GO enrichment analysis

In mzinkgraf/treeGO: GO enrichment analysis for tree species

Description

This function does GO enrichment on a user defined GO universe

Usage

GOanalysis(genes, universe = pt210_GO_Universe,
               organism = "Populus trichocarpa", pv = 0.01,
               ontology=c("BP","MF","CC"), testDirection = "over",
               conditional=FALSE)

Arguments

genes	Provide a vector of gene names to be tested
universe	Provide a user define GO universe
organism	Specify the name of the organism
pv	Specify a p-value threshhold for significance (default = 0.01)
ontology	Specify the ontologies to test (Default = c("BP","MF","CC"))
testDirection	A string which can be either "over" or "under". This determines whether the test performed detects over or under represented GO terms. See GSEAGOHyperGParams (Defalut = "over")
conditional	A logical indicating whether the calculation should condition on the GO structure. (GO only)

Value

Returns a list object that contains the ontology results for Biological Processes (BP), Molecular Functions (MF) and Cellular Components (CC)

Author(s)

Matthew Zinkgraf, [e-mail]

mzinkgraf/treeGO documentation built on May 24, 2019, 6:10 a.m.