HyperGParams-class: Class "HyperGParams"
In Category: Category Analysis

Description Objects from the Class Slots Methods Author(s) See Also

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

Objects of this class cannot be instantiated directly.

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:: Object of class "ANY". Functionally, this is either a string giving the name of the annotation data package for the chip used to generate the data, or the name of an annotation object downloaded using AnnotationHub.
categorySubsetIds:: 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".
pvalueCutoff:: The p-value to use as a cutoff for significance for testing methods that require it. This value will also be passed on to the result instance and used for display and counting of significant results. The default is 0.01.
testDirection:: A string indicating whether the test should be for overrepresentation ("over") or underrepresentation ("under").
datPkg:: Holds a DatPkg object which is of a particular type that in turn varies with the kind of annotation package this is.

hyperGTest: signature(p = "HyperGParams"): 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 HyperGParams.
geneIds(object), geneIds(object) <- value: Accessors for the gene identifiers that will be used as the selected gene list.
codeannotation(object): Accessor for annotation. If you want to change the annotation for an existing instance, use the replacement form.
ontology(object): Accessor for GO ontology.
organism(object): Accessor for the organism character string used as an identifier in DatPkg.
pvalueCutoff(r), pvalueCutoff(r) <- value: Accessor for the p-value cutoff. When setting, value should be a numeric value between zero and one.
testDirection: Accessor for the test direction. When setting, value must be either "over" or "under".
universeGeneIds(r): accessor for vector of gene identifiers.