LinearMParams-class: Class "LinearMParams"

In Bioconductor/Category: Category Analysis

Class "LinearMParams"

Description

A parameter class for representing all parameters needed by a method specializing the linearMTest generic.

Objects from the Class

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

Slots

geneStats:

Named vector of class "numeric", giving the gene-level statistics to be used in the tests. The names should correspond to the gene identifiers in gsc.

universeGeneIds:

Object of class "ANY": A vector of gene ids 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. Currently this parameter is ignored by the base linearMTest method.

annotation:

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

datPkg:

Object of class "DatPkg" used to assist with dispatch based on type of annotation data available. Currently this parameter is ignored by the base linearMTest method.

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. Currently this parameter is ignored by the base linearMTest method.

categoryName:

A string describing the category. Usually set automatically by subclasses. For example "ChrMap".

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.

minSize:

An integer giving a minimum size for a gene set for it to be tested. The default is 5.

testDirection:

A string indicating whether the test should test for systematic increase ("up") or decrease ("down") in the geneStats values within a gene set relative to the remaining genes.

graph:

The graph object indicating the hierarchical relationship among terms of the ontology or other grouping.

conditional:

A logical indicating whether conditional tests should be performed. This tests whether a term is still significant even when including its sub-terms in the model.

gsc:

The GeneSetCollection object grouping the gene ids into sets.

Methods

These are accessor methods for the various parameter slots:

annotation<-

signature(object = "LinearMParams", value = "character"): ...

annotation

signature(object = "LinearMParams"): ...

categoryName

signature(r = "LinearMParams"): ...

conditional

signature(r = "LinearMParams"): ...

geneIds<-

signature(object = "LinearMParams"): ...

geneIds

signature(object = "LinearMParams"): ...

pvalueCutoff<-

signature(r = "LinearMParams"): ...

pvalueCutoff

signature(r = "LinearMParams"): ...

show

signature(object = "LinearMParams"): ...

testDirection<-

signature(r = "LinearMParams"): ...

testDirection

signature(r = "LinearMParams"): ...

conditional<-

signature(r = "LinearMParams"): ...

conditional

signature(r = "LinearMParams"): ...

universeGeneIds

signature(r = "LinearMParams"): ...

Author(s)

Deepayan Sarkar, Michael Lawrence

See Also

See linearMTest for examples. ChrMapLinearMParams is a specialization of this class for chromosome maps.

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