geneSets: Retrieve or Determine Gene Sets

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

Retrieve or Determine Gene Sets

Description

Retrieves or determines the gene sets that have been used or would be used in a gsva() gene set analysis. These are not necessarily the same as the input gene sets. See Details.

Usage

## S4 method for signature 'GsvaMethodParam'
geneSets(obj)

## S4 method for signature 'SummarizedExperiment'
geneSets(obj)

## S4 method for signature 'SingleCellExperiment'
geneSets(obj)

## S4 method for signature 'SpatialExperiment'
geneSets(obj)

## S4 method for signature 'GsvaExprData'
geneSets(obj)

## S4 method for signature 'GsvaMethodParam'
geneSetSizes(obj)

## S4 method for signature 'GsvaExprData'
geneSetSizes(obj)

Arguments

obj	An object of one of the following classes: An expression data object of one of the classes described in GsvaExprData that is the return value of a call to gsva(). A parameter object of one of the classes described in GsvaMethodParam that could be used in a call to gsva().

Details

The gene sets used in a gsva() gene set analysis, or just their sizes, may be a valuable input to subsequent analyses. However, they are not necessarily the same as the original input gene sets, or their sizes: based on user choices, the gene annotation used, or presence/absence of genes in gene sets and expression data set, gsva() may have to modify them during the preparation of an analysis run. In order to make use of these gene sets or their sizes, you can either

• retrieve them from the object returned by gsva() by passing this object to geneSets() or geneSetSizes(), or

• predict them by calling geneSets() or geneSetSizes() on the parameter object that would also be passed to gsva(). This is much slower and should only be done if you do not intend to run an actual gene set analysis.

geneSetSizes() is a convenience wrapper running lengths() on the list of gene sets returned by geneSets().

Value

The geneSets() methods return a named list of character vectors where each character vector contains the gene IDs of a gene set. The geneSetSizes() methods return a named integer vector of gene set sizes.

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