gsvaAnnotation: Store and Retrieve Annotation Metadata

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

Store and Retrieve Annotation Metadata

Description

Methods for storing and retrieving annotation metadata in expression data objects that support it. If gene sets and expression data are using different but known gene identifier types and an appropriate annotation database is available, gene set identifiers can be mapped to expression data identifiers without manual user intervention, e.g. from an MSigDb gene set using ENTREZ IDs or gene symbols to an expression data set using ENSEMBL IDs.

Usage

## S4 method for signature 'GsvaExprData'
gsvaAnnotation(object)

## S4 replacement method for signature 'GsvaExprData,GeneIdentifierType'
gsvaAnnotation(object) <- value

## S4 method for signature 'ExpressionSet'
gsvaAnnotation(object)

## S4 replacement method for signature 'ExpressionSet,character'
gsvaAnnotation(object) <- value

## S4 replacement method for signature 'ExpressionSet,GeneIdentifierType'
gsvaAnnotation(object) <- value

## S4 method for signature 'SummarizedExperiment'
gsvaAnnotation(object)

## S4 replacement method for signature 'SummarizedExperiment,GeneIdentifierType'
gsvaAnnotation(object) <- value

## S4 method for signature 'SingleCellExperiment'
gsvaAnnotation(object)

## S4 replacement method for signature 'SingleCellExperiment,GeneIdentifierType'
gsvaAnnotation(object) <- value

## S4 method for signature 'SpatialExperiment'
gsvaAnnotation(object)

## S4 replacement method for signature 'SpatialExperiment,GeneIdentifierType'
gsvaAnnotation(object) <- value

## S4 method for signature 'list'
gsvaAnnotation(object)

## S4 replacement method for signature 'list,GeneIdentifierType'
gsvaAnnotation(object) <- value

## S4 method for signature 'GeneSetCollection'
gsvaAnnotation(object)

Arguments

object

An expression data object of one of the classes described in GsvaExprData. Simple matrix and dgCMatrix objects are not capable of storing annotation metadata and will return NULL.

value

For the replacement methods, the annotation metadata to be stored in the object. For ExpressionSet objects, this must be a character of length 1 specifying the name of the annotation database to be used. For SummarizedExperiment and its subclasses, this must be a GeneIdentifierType created by one of the constructors from package GSEABase where the annotation argument is typically the name of an organism or annotation database, e.g. org.Hs.eg.db. Simple matrix and dgCMatrix objects are not capable of storing annotation metadata and the attempt to do so will result in an error.

Value

For the retrieval methods, the annotation metadata stored in the object of NULL. For the replacement methods, the updated object.

rcastelo/GSVA documentation built on Nov. 12, 2024, 10:08 a.m.