KEGGHyperGParams-class: Class "KEGGHyperGParams" and "PFAMHyperGParams"
In Bioconductor/Category: Category Analysis

KEGGHyperGParams-class

R Documentation

Class "KEGGHyperGParams" and "PFAMHyperGParams"

Parameter classes for representing all parameters needed for running the hyperGTest method with KEGG or PFAM as the category.

Objects can be created by calls of the form new("KEGGHyperGParams", ...) or new("PFAMHyperGParams", ...).

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. This will be automatically set to "KEGG" or "PFAM" via the class's prototype.
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").

Class "HyperGParams", directly.

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.

S. Falcon