go_annot_download {OmnipathR} | R Documentation

## Gene annotations from Gene Ontology

### Description

Gene Ontology is an ontology of gene subcellular localizations, molecular functions and involvement in biological processes. Gene products across many organisms are annotated with the ontology terms. This function downloads the gene-ontology term associations for certain model organisms or all organisms. For a description of the columns see http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/.

### Usage

    go_annot_download(organism = "human", aspects = c("C", "F", "P"), slim = NULL)

### Arguments

`organism` | Character: either "chicken", "cow", "dog", "human", "pig" or "uniprot_all".
`aspects` | Character vector with some of the following elements: "C" (cellular component), "F" (molecular function) and "P" (biological process). Gene Ontology is three separate ontologies called as three aspects. By this parameter you can control which aspects to include in the output.
`slim` | Character: if not `NULL`, the name of a GOsubset (slim). instead of the full GO annotation, the slim annotation will be returned. See details at `go_annot_slim`. If `TRUE`, the "generic" slim will be used.

### Value

A tibble (data frame) of annotations as it is provided by the database

### Examples

    goa_data <- go_annot_download()
    goa_data
    # # A tibble: 606,840 x 17
    #    db       db_object_id db_object_symbol qualifier go_id   db_ref
    #    <fct>    <chr>        <chr>            <fct>     <chr>   <chr>
    #  1 UniProt. A0A024RBG1   NUDT4B           NA        GO:000. GO_REF:00.
    #  2 UniProt. A0A024RBG1   NUDT4B           NA        GO:000. GO_REF:00.
    #  3 UniProt. A0A024RBG1   NUDT4B           NA        GO:004. GO_REF:00.
    #  4 UniProt. A0A024RBG1   NUDT4B           NA        GO:005. GO_REF:00.
    #  5 UniProt. A0A024RBG1   NUDT4B           NA        GO:005. GO_REF:00.
    # # . with 606,830 more rows, and 11 more variables:
    # #   evidence_code <fct>, with_or_from <chr>, aspect <fct>,
    # #   db_object_name <chr>, db_object_synonym <chr>,
    # #   db_object_type <fct>, taxon <fct>, date <date>,
    # #   assigned_by <fct>, annotation_extension <chr>,
    # #   gene_product_from_id <chr>

[Package OmnipathR version 3.0.0 Index]