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Category (version 2.38.0)

GSEAGOHyperGParams: Helper function for constructing a GOHyperGParams objects or KEGGHyperGParams objects from a GeneSetCollection

Description

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.

Usage

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


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

Arguments

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.

See Also

HyperGResult-class GOHyperGParams-class hyperGTest