hgParams: A wrapper function to build a parameter class for the input...
In ppiStats: Protein-Protein Interaction Statistical Package

Description Usage Arguments Value Author(s)

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.

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)

`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.