HyperGResult-class: Class "HyperGResult"

In Bioconductor/Category: Category Analysis

Class "HyperGResult"

Description

This class represents the results of a test for over-representation of categories among genes in a selected gene set based upon the Hypergeometric distribution. The hyperGTest generic function returns an instance of the HyperGResult class. For details on accessing the results, see HyperGResult-accessors.

Objects from the Class

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

Slots

pvalues:

"numeric" vector: the ordered p-values for each category term tested.

catToGeneId:

Object of class "list". The names of the list are category IDs. Each element is a vector of gene IDs annotated at the given category ID and in the specified gene universe.

annotation:

A string giving the name of the chip annotation data package used.

geneIds:

Object of class "ANY": the input vector of gene identifiers intersected with the universe of gene identifiers used in the computation. The class of this slot is specified as "ANY" because gene IDs may be integer or character vectors depending on the annotation package.

testName:

A string identifying the testing method used.

pvalueCutoff:

Numeric value used a a p-value cutoff. Used by the show method to count number of significant terms.

testDirection:

A string indicating whether the test should be for overrepresentation ("over") or underrepresentation ("under").

oddsRatios

a "numeric" vector giving the odds ratio for each category term tested.

expectedCounts

a "numeric" vector giving the expected number of genes in the selected gene list to be found at each tested category term.

Extends

Class "HyperGResultBase", directly.

Methods

See HyperGResult-accessors.

Author(s)

Seth Falcon

See Also

HyperGResultBase-class GOHyperGResult-class HyperGResult-accessors

Bioconductor/Category documentation built on Nov. 2, 2024, 6:33 a.m.