GeneCategoryHyperGeoTestResult-class {Category}R Documentation

Class "GeneCategoryHyperGeoTestResult"

Description

This class represents the results of a test for overrepresentation of categories among genes in a selected gene set based upon the Hypergeometric distribution. The geneCategoryHyperGeoTest generic function returns an instance of the GeneCategoryHyperGeoTestResult class.

Objects from the Class

Objects can be created by calls of the form new("GeneCategoryHyperGeoTestResult", ...).

Slots

pvalues:
"numeric" vector: the ordered p-values for each category term tested.
geneCounts:
"integer" vector: for each category term tested, the number of genes from the gene set that are annotated at the term.
universeCounts:
"integer" vector: for each category term tested, the number of genes from the gene universe that are annotated at the term.
universeMappedCount:
"integer" vector of length one: The size of the gene universe set.
geneMappedCount:
"integer" vector of length one: The size of the selected gene set.
annotation:
A string giving the name of the chip annotation data package used.
geneIds:
Object of class "ANY": the input vector of gene identifiers passed to the testing method.
testName:
A string identifying the testing method used.

Methods

show
signature(object = "GeneCategoryHyperGeoTestResult"): Display a short summary of the result

Author(s)

S. Falcon

See Also

geneCategoryHyperGeoTest phyper


[Package Category version 1.4.1 Index]