GeneSet-methods: GeneSet methods

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

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)

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: XML
Loading required package: graph

Attaching package: ‘graph’

The following object is masked from ‘package:XML’:

    addNode

[1] 20
geneSet1 geneSet2 
      20        5 
GeneSetCollection
  names: geneSet1, geneSet2 (2 total)
  unique identifiers: Gene15, Gene16, ..., Gene20 (6 total)
  types in collection:
    geneIdType: NullIdentifier (1 total)
    collectionType: NullCollection (1 total)
[1] "one" "two"

AUCell documentation built on Nov. 8, 2020, 5:51 p.m.