get_ids {GOfuncR} | R Documentation

## Get the ID of a GO-category given its name

### Description

Returns GO-categories given (part of) their name. Matching is not case-sensitive.

### Usage

        get_ids(go_name, term_df = NULL, godir = NULL)

### Arguments

`go_name` | character(). (partial) name of a GO-category
`term_df` | optional data.frame() with an ontology 'term' table. Alternative to the default integrated GO-graph or `godir`.
`godir` | optional character() specifying a directory that contains the ontology table 'term.txt'. Alternative to the default integrated GO-graph or `term_df`.

### Details

For details on how to use a custom ontology with `term_df` or `godir` please refer to the package's vignette. The advantage of `term_df` over `godir` is that the latter reads the file 'term.txt' from disk and therefore takes longer.

### Value

a data.frame() with three columns: the full names (character()) of the GO-categories that contain `go_name`; together with the GO-domain ('cellular_component', 'biological_process' or 'molecular_function') and the GO-category IDs (character()).

### Note

This is just a `grep(..., ignore.case=TRUE)` on the node names of the ontology.
More sophisticated searches, e.g. with regular expressions, could be performed on the table returned by `get_ids('')` which lists all non-obsolete GO-categories.

### Author(s)

Steffi Grote

### References

[1] Ashburner, M. et al. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics 25, 25-29.

### See Also

`get_names`
`get_parent_nodes`
`get_child_nodes`

### Examples

    ## get GO-IDs of categories that contain 'gabaergic' in their names
    get_ids('gabaergic')

    ## get GO-IDs of categories that contain 'blood-brain barrier' in their names
    get_ids('blood-brain barrier')

    ## get all valid GO-categories
    all_nodes = get_ids('')
    head(all_nodes)

[Package GOfuncR version 1.6.1 Index]