atGOanalysis: GO enrichment analysis using Arabidopsis TAIR10

In mzinkgraf/treeGO: GO enrichment analysis for tree species

Description

This function does GO enrichment on TAIR10 GO universe

Usage

atGOanalysis(genes, universe = TAIR10_GO_Universe,
               organism = "Arabidopsis thaliana", pv = 0.01,
               ontology=c("BP","MF","CC"), testDirection = "over")

Arguments

genes	Provide a vector of gene names to be tested
universe	Arabidopsis TAIR10 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")

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.