GeneCategoryHyperGeoTestParams-class {Category}R Documentation

Class "GeneCategoryHyperGeoTestParams"

Description

An abstract (VIRTUAL) parameter class for representing all parameters needed by a method specializing the geneCategoryHyperGeoTest generic. You should only use subclasses of this class directly.

Objects from the Class

Objects of this class cannot be instantiated directly.

Slots

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.
annotation:
A string giving the name of the annotation data package for the chip used to generate the data.
cateogrySubsetIds:
Object of class "ANY": If the test method supports it, can be used to specify a subset of category ids to include in the test instead of all possible category ids.
categoryName:
A string describing the category. Usually set automatically by subclasses. For example "GO".

Methods

geneCategoryHyperGeoTest
signature(p = "GeneCategoryHyperGeoTestParams"): Perform hypergeometric tests to assess overrepresentation of category ids in the gene set. See the documentation for the generic function for details. This method must be called with a proper subclass of GeneCategoryHyperGeoTestParams.

Author(s)

S. Falcon

See Also

GeneCategoryHyperGeoTestResult-class GeneGoHyperGeoTestParams-class GeneKeggHyperGeoTestParams-class geneKeggHyperGeoTest geneCategoryHyperGeoTest


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