GsvaMethodParam-class: 'GsvaMethodParam' class

In rcastelo/GSVA: Gene Set Variation Analysis for Microarray and RNA-Seq Data

GsvaMethodParam class

Description

Virtual superclass of method parameter classes supported by GSVA.

A virtual superclass of the GSVA packages' method-specific parameter classes.

Details

GSVA implements four single-sample gene set analysis methods: PLAGE, combined z-scores, ssGSEA, and GSVA. All of them take at least an expression data matrix and one or more gene sets as input. Further common parameters include an assay name for use with multi-assay expression data containers, the gene ID type used by the expression data set, and a minimum and maximum size for gene sets to limit the range of gene set sizes used in an analysis. This virtual class provides the necessary slots for this shared parameter set and serves as the parent class for all GSVA method parameter classes.

The GSVA package implements four single-sample gene set analysis methods (PLAGE, combined z-scores, ssGSEA, and GSVA) and a respective method-specific parameter class that is used to invoke each of them with a matching set of parameters.

Slots

exprData

The expression data set. Must be one of the classes supported by GsvaExprData. For a list of these classes, see its help page using help(GsvaExprData).

geneSets

The gene sets. Must be one of the classes supported by GsvaGeneSets. For a list of these classes, see its help page using help(GsvaGeneSets).

assay

Character vector of length 1. The name of the assay to use in case exprData is a multi-assay container, otherwise ignored. By default, the first assay is used.

annotation

An object of class GeneIdentifierType from package GSEABase describing the gene identifiers used as the row names of the expression data set. See GeneIdentifierType for help on available gene identifier types and how to construct them. This information can be used to map gene identifiers occurring in the gene sets. By default, this slot has value NullIdentifier and gene identifiers used in expression data set and gene sets are matched directly.

minSize

Numeric vector of length 1. Minimum size of the resulting gene sets after gene identifier mapping. By default, the minimum size is 1.

maxSize

Numeric vector of length 1. Maximum size of the resulting gene sets after gene identifier mapping. By default, the maximum size is Inf.

See Also

GsvaExprData, GsvaGeneSets, zscoreParam, plageParam, ssgseaParam, gsvaParam, GeneIdentifierType GeneIdentifierType

plageParam, zscoreParam, ssgseaParam, gsvaParam

rcastelo/GSVA documentation built on Dec. 17, 2024, 4:51 p.m.