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", "msigdb", "enrichr"),
      gene.id.type = "ENTREZID",
      cache = TRUE,
      return.type = c("list", "GeneSetCollection"),
      ...
    )

    showAvailableSpecies(db = c("go", "kegg", "msigdb", "enrichr"), cache = TRUE)

    showAvailableCollections(
      org,
      db = c("go", "kegg", "msigdb", "enrichr"),
      cache = TRUE
    )

    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), 'kegg', 'msigdb', or 'enrichr'.
`gene.id.type` | Character. Gene ID type of the returned gene sets. Defaults to `"ENTREZID"`. See `idTypes` for available gene ID types.
`cache` | Logical. Should a locally cached version used if available? Defaults to `TRUE`.
`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`.
`...` | Additional arguments for individual gene set databases. For `db = "GO"`: onto: Character. Specifies one of the three GO ontologies: 'BP' (biological process), 'MF' (molecular function), 'CC' (cellular component). Defaults to 'BP'. evid: Character. Specifies one or more GO evidence code(s) such as IEP (inferred from expression pattern) or TAS (traceable author statement). Defaults to `NULL` which includes all annotations, i.e. does not filter by evidence codes. See references for a list of available evidence codes. hierarchical: Logical. Incorporate hierarchical relationships between GO terms ('is_a' and 'has_a') when collecting genes annotated to a GO term? If set to `TRUE`, this will return all genes annotated to a GO term *or to one of its child terms* in the GO ontology. Defaults to `FALSE`, which will then only collect genes directly annotated to a GO term. 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'. For `db = "msigdb":` cat: Character. MSigDB collection category: 'H' (hallmark), 'C1' (genomic position), 'C2' (curated databases), 'C3' (binding site motifs), 'C4' (computational cancer), 'C5' (Gene Ontology), 'C6' (oncogenic), 'C7' (immunologic). See references. subcat: Character. MSigDB collection subcategory. Depends on the chosen MSigDB collection category. For example, 'MIR' to obtain microRNA targets from the 'C3' collection. See references. For `db = "enrichr"`: lib: Character. Enrichr gene set library. For example, 'Genes_Associated_with_NIH_Grants' to obtain gene sets based on associations with NIH grants. See references.
`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.

For `showAvailableSpecies` and `showAvailableCollections`: a `DataFrame`, displaying supported species and available gene set collections for a gene set database of choice.

### Author(s)

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

### References

GO: http://geneontology.org/

GO evidence codes: http://geneontology.org/docs/guide-go-evidence-codes/

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

MSigDB: http://software.broadinstitute.org/gsea/msigdb/collections.jsp

Enrichr: https://maayanlab.cloud/Enrichr/#stats

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

### See Also

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

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

`msigdbr::msigdbr` for obtaining gene sets from the MSigDB.

### 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", onto = "BP", mode = "GO.db")

        # Alternatively:
        # downloading from BioMart
        # this may take a few minutes ...
        go.gs <- getGenesets(org = "hsa", db = "go", mode = "biomart")

        # list supported species for obtaining gene sets from GO
        showAvailableSpecies(db = "go")

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

        # list supported species for obtaining gene sets from KEGG
        showAvailableSpecies(db = "kegg")

        # (3) Obtaining *H*allmark gene sets from MSigDB
        hall.gs <- getGenesets(org = "hsa", db = "msigdb", cat = "H")

        # list supported species for obtaining gene sets from MSigDB
        showAvailableSpecies(db = "msigdb")

        # list available gene set collections in the MSigDB
        showAvailableCollections(db = "msigdb")

        # (4) Obtaining gene sets from Enrichr
        tfppi.gs <- getGenesets(org = "hsa", db = "enrichr",
                                lib = "Transcription_Factor_PPIs")

        # list supported species for obtaining gene sets from Enrichr
        showAvailableSpecies(db = "enrichr")

        # list available Enrichr gene set libraries
        showAvailableCollections(org = "hsa", db = "enrichr")

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

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

[Package EnrichmentBrowser version 2.20.7 Index]