GeneSet-methods: GeneSet methods

In aertslab/AUCell: AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

GeneSet methods

Description

Functions to manipulate GeneSet and GeneSetCollection objects (from package GSEABase)

Usage

nGenes(geneSet)

## S4 method for signature 'GeneSet'
nGenes(geneSet)

## S4 method for signature 'GeneSetCollection'
nGenes(geneSet)

subsetGeneSets(geneSets, geneNames)

## S4 method for signature 'GeneSetCollection'
subsetGeneSets(geneSets, geneNames)

setGeneSetNames(geneSets, newNames)

## S4 method for signature 'GeneSetCollection'
setGeneSetNames(geneSets, newNames)

Arguments

geneSet	One gene-set (GeneSet)
geneSets	Gene-set collection (GeneSetCollection)
geneNames	Gene names (for subset)
newNames	New names (to assign to the gene sets)

Value

- **nGenes()**: provides the number of genes in the gene-set, or each of the gene-sets in a collection

- **subsetGeneSets()**: Subsets each of the gene-sets in a collection to contain only the genes inthe given list. Equivalent to intersect(), but keeping the original gene-set name.

- **setGeneSetNames()**: Modifies the name of each gene-set in a collection

Examples

library(GSEABase)
genes_1 <- GeneSet(paste("Gene", 1:20, sep=""), setName="geneSet1")
genes_2 <- GeneSet(paste("Gene", 18:22, sep=""), setName="geneSet2")
geneSets <- GeneSetCollection(genes_1, genes_2)

nGenes(genes_1)
nGenes(geneSets)

subsetGeneSets(geneSets, paste("Gene", 15:20, sep=""))

geneSets_newNames <- setGeneSetNames(geneSets, c("one", "two"))
names(geneSets_newNames)

aertslab/AUCell documentation built on March 12, 2024, 11:40 p.m.