GeneSet {GSEABase} | R Documentation

## Methods to construct GeneSet instances

### 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)

[Package GSEABase version 1.54.0 Index]