GeneSet-methods: Methods to construct GeneSet instances

In GSEABase: Gene set enrichment data structures and methods

Description

Use GeneSet to construct gene sets from ExpressionSet, character vector, or other objects.

Usage

GeneSet(type, ..., setIdentifier=.uniqueIdentifier())

Arguments

type	An argument determining how the gene set will be created, as described in the Methods section.
setIdentifier	A ScalarCharacter or length-1 character vector uniquely identifying the set.
...	Additional arguments for gene set construction. Methods have required arguments, as outlined below; additional arguments correspond to slot names GeneSet.

Methods

signature(type = "missing", ..., setIdentifier=.uniqueIdentifier())

Construct an empty gene set.

signature(type = "character", ..., setIdentifier=.uniqueIdentifier())

Construct a gene set using identifiers type.

signature(type = "GeneIdentifierType", ..., setIdentifier=.uniqueIdentifier())

Construct an empty gene set. The gene set has geneIdType created from the GeneIdentifierType of type.

signature(type = "ExpressionSet", ..., setIdentifier=.uniqueIdentifier())

Construct a gene set from an ExpressionSet. geneIdType is set to AnnotationIdentifier; the annotation field and annotation package of the ExpressionSet are consulted to determine organism, if possible. Short and long descriptions from the ExpressionSet experimentData title and abstract; pub med ids, urls, and contributor are also derived from experimentData.

signature(type = "GOCollection", ..., geneIdType, setIdentifier=.uniqueIdentifier())

Use genes contained in type to create a GeneSet . The required arugment geneIdType must include a package for which an appropriate map (to GO) exists, e.g., EntrezIdentifier('org.Hs.eg.db').

signature(type = "BroadCollection", ..., urls = character(0), setIdentifier=.uniqueIdentifier())

Read XML following the Broad Institute schema and located at urls to create a gene set. The url can be a local file or internet connection, but must contain just a single gene set. See getBroadSets for details.

See Also

GeneSet-class GeneColorSet-class

Examples

## Empty gene set
GeneSet()

## Gene set from ExpressionSet
data(sample.ExpressionSet)
gs1 <- GeneSet(sample.ExpressionSet[100:109])

## GeneSet from Broad XML; 'fl' could be a url
fl <- system.file("extdata", "Broad.xml", package="GSEABase")
gs2 <- getBroadSets(fl)[[1]] # actually, a list of two gene sets

## GeneSet from list of gene identifiers
geneIds <- geneIds(gs2) # any character vector would do
gs3 <- GeneSet(geneIds)
## unspecified set type, so...
is(geneIdType(gs3), "NullIdentifier") == TRUE
## update set type to match encoding of identifiers
geneIdType(gs2)
geneIdType(gs3) <- SymbolIdentifier()
## other ways of accomplishing the same
gs4 <- GeneSet(geneIds, geneIdType=SymbolIdentifier())
gs5 <- GeneSet(SymbolIdentifier(), geneIds=geneIds)

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

setName: NA 
geneIds:  (total: 0)
geneIdType: Null
collectionType: Null 
details: use 'details(object)'


[1] TRUE
geneIdType: Symbol

GSEABase documentation built on Dec. 13, 2020, 2 a.m.