getGenesets {EnrichmentBrowser} | R Documentation

## Definition of gene sets according to different sources

### Description

Functionality for retrieving gene sets for an organism under investigation from databases such as GO and KEGG. Parsing and writing a list of gene sets from/to a flat text file in GMT format is also supported.

The GMT (Gene Matrix Transposed) file format is a tab delimited file format that describes gene sets. In the GMT format, each row represents a gene set. Each gene set is described by a name, a description, and the genes in the gene set. See references.

### Usage

    getGenesets(org, db = c("go", "kegg"), cache = TRUE,
      go.onto = c("BP", "MF", "CC"), go.mode = c("GO.db", "biomart"),
      return.type = c("list", "GeneSetCollection"))

    writeGMT(gs, gmt.file)

### Arguments

`org` | An organism in (KEGG) three letter code, e.g. ‘hsa’ for ‘Homo sapiens’. Alternatively, this can also be a text file storing gene sets in GMT format. See details.
`db` | Database from which gene sets should be retrieved. Currently, either 'go' (default) or 'kegg'.
`cache` | Logical. Should a locally cached version used if available? Defaults to `TRUE`.
`go.onto` | Character. Specifies one of the three GO ontologies: 'BP' (biological process), 'MF' (molecular function), 'CC' (cellular component). Defaults to 'BP'.
`go.mode` | Character. Determines in which way the gene sets are retrieved. This can be either 'GO.db' or 'biomart'. The 'GO.db' mode creates the gene sets based on BioC annotation packages - which is fast, but represents not necessarily the most up-to-date mapping. In addition, this option is only available for the currently supported model organisms in BioC. The 'biomart' mode downloads the mapping from BioMart - which can be time consuming, but allows to select from a larger range of organisms and contains the latest mappings. Defaults to 'GO.db'.
`return.type` | Character. Determines whether gene sets are returned as a simple list of gene sets (each being a character vector of gene IDs), or as an object of class `GeneSetCollection`.
`gs` | A list of gene sets (character vectors of gene IDs).
`gmt.file` | Gene set file in GMT format. See details.

### Value

For `getGenesets`: a list of gene sets (vectors of gene IDs). For `writeGMT`: none, writes to file.

### Author(s)

Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>

### References

GO: http://geneontology.org/

KEGG Organism code http://www.genome.jp/kegg/catalog/org_list.html

GMT file format http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats

### See Also

`annFUN` for general GO2gene mapping used in the 'GO.db' mode, and the biomaRt package for general queries to BioMart.

`keggList` and `keggLink` for accessing the KEGG REST server.

### Examples

        # (1) Typical usage for gene set enrichment analysis with GO:
        # Biological process terms based on BioC annotation (for human)
        go.gs <- getGenesets(org="hsa", db="go")

        # eq.:
        # go.gs <- getGenesets(org="hsa", db="go", go.onto="BP", go.mode="GO.db")

        # Alternatively:
        # downloading from BioMart
        # this may take a few minutes ...

         go.gs <- getGenesets(org="hsa", db="go", mode="biomart")

        # (2) Defining gene sets according to KEGG
        kegg.gs <- getGenesets(org="hsa", db="kegg")

        # (3) parsing gene sets from GMT
        gmt.file <- system.file("extdata/hsa_kegg_gs.gmt", package="EnrichmentBrowser")
        gs <- getGenesets(gmt.file)

        # (4) writing gene sets to file
        writeGMT(gs, gmt.file)

[Package EnrichmentBrowser version 2.14.3 Index]