GOHyperGParams-class: Class "GOHyperGParams"

In Bioconductor/Category: Category Analysis

Class "GOHyperGParams"

Description

A parameter class for representing all parameters needed for running the hyperGTest method with one of the GO ontologies (BP, CC, MF) as the category.

Objects from the Class

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

Slots

ontology:

A string specifying the GO ontology to use. Must be one of "BP", "CC", or "MF".

conditional:

A logical indicating whether the calculation should condition on the GO structure.

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.

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".

datPkg:

Holds a DatPkg object which is of a particular type that in turn varies with the kind of annotation package this is.

pvalueCutoff:

A numeric values between zero and one used as a p-value cutoff for p-values generated by the Hypergeometric test. When the test being performed is non-conditional, this is only used as a default value for printing and summarizing the results. For a conditional analysis, the cutoff is used during the computation to determine perform the conditioning: child terms with a p-value less than pvalueCutoff are conditioned out of the test for their parent term.

orCutoff:

A numeric value used as an odds-ratio cutoff for odds ratios generated by the conditional Hypergeometric test. For such a test, it works like the pvalueCutoff but applied on the odds ratio. It has no effect when conditional=FALSE.

minSizeCutoff:

A numeric value used as a cutoff for minimum size of the gene sets being tested with the conditional Hypergeometric test. For such a test, it works like the pvalueCutoff but applied on the odds ratio. It has no effect when conditional=FALSE.

maxSizeCutoff:

A numeric value used as a cutoff for maximum size of the gene sets being tested with the conditional Hypergeometric test. For such a test, it works like the pvalueCutoff but applied on the odds ratio. It has no effect when conditional=FALSE.

testDirection:

A string which can be either "over" or "under". This determines whether the test performed detects over or under represented GO terms.

Extends

Class "HyperGParams", directly.

Methods

hyperGTest(p)

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.

ontology(p), ontology(p) <- value

Accessors for the GO ontology. When setting, value should be one of "BP", "CC", or "MF".

conditional(p), conditional(p) <- value

Accessors for the conditional flag. When setting, value must be TRUE or FALSE.

Author(s)

S. Falcon

See Also

HyperGResult-class GOHyperGParams-class hyperGTest

Bioconductor/Category documentation built on Oct. 29, 2023, 4:15 p.m.