GSEAGOHyperGParams: Helper function for constructing a GOHyperGParams objects or...
In Category: Category Analysis

Description Usage Arguments Author(s) See Also

Helps to create A parameter class for representing all parameters needed for running the hyperGTest method. If it is a GOHyperGParams object, being made, then with one of the GO ontologies (BP, CC, MF) as the category. This function will construct the parameter object from a GeneSetCollection object and if necessary will also try to check to make sure that the object is based on a GO2ALL mapping.

  GSEAGOHyperGParams(name, geneSetCollection, geneIds, universeGeneIds,
  ontology, pvalueCutoff, conditional, testDirection, ...)

  GSEAKEGGHyperGParams(name, geneSetCollection, geneIds, universeGeneIds,
  pvalueCutoff, testDirection, ...)

`name`	String specifying name of the GeneSetCollection.
`geneSetCollection`	A GeneSetCollection Object. If a GOHyperGParams object is sought, then this GeneSetCollection should be based on a GO2ALLFrame object and so the idType of that GeneSetCollection should be GOAllFrameIdentifier. If a KEGGHyperGParams object is sought then a GeneSetCollection based on a KEGGFrame object should be used and the idType will be a KEGGFrameIdentifier.
`geneIds`	Object of class `"ANY"`: A vector of gene identifiers. Numeric and character vectors are probably the only things that make sense. These are the gene ids for the selected gene set.
`universeGeneIds`	Object of class `"ANY"`: A vector of gene ids in the same format as `geneIds` defining a subset of the gene ids on the chip that will be used as the universe for the hypergeometric calculation. If this is `NULL` or has length zero, then all gene ids on the chip will be used.
`ontology`	A string specifying the GO ontology to use. Must be one of "BP", "CC", or "MF". (used with GO only)
`pvalueCutoff`	A numeric values between zero and one used as a p-value cutoff for p-values generated by the Hypergeometric test. When the test being performed is non-conditional, this is only used as a default value for printing and summarizing the results. For a conditional analysis, the cutoff is used during the computation to determine perform the conditioning: child terms with a p-value less than pvalueCutoff are conditioned out of the test for their parent term.
`conditional`	A logical indicating whether the calculation should condition on the GO structure. (GO only)
`testDirection`	A string which can be either "over" or "under". This determines whether the test performed detects over or under represented GO terms.
`...`	optional arguments to configure the GOHyperGParams object.