A wrapper function to build a parameter class for the input of the HyperGTest.

Description

This function takes a gene set and conducts test for either over or under representation of some category using the Hypergeometric distribution.

The two differences when building the parameter classes are that a conditional test can be performed on the GO dag but not on PFAM categories and an ontology can be assigned to GO but not to PFAM.

Usage

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ppiBuildParams4GO(geneSet, universe, direction="over", annot="org.Sc.sgd",
                           ontology = "CC", cond=TRUE, pThresh = 0.01)
ppiBuildParams4PFAM(geneSet, universe, annot ="org.Sc.sgd",
                              direction = "over", pThresh=0.01)

Arguments

geneSet

A character vector of genes given by the gene locus name.

universe

The set of genes by which the geneSet is tested against for over/under representation. The genes are also given by the gene locus names.

direction

A character. This parameter can be either set to over or under when testing for GO categories.

annot

A character. The annotation package used.

ontology

A character: either CC, MF, or BP to describe the GO ontology.

cond

A logical. To test within the CO dag, a conditional hypergeometric test can be conducted.

pThresh

A numeric. A p-value threshold by which the null hypothesis is rejected.

Value

A object of class hyperGParams.

Author(s)

T Chiang

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