ancestors {OmnipathR} | R Documentation

## All ancestors in the ontology tree

### Description

Starting from the selected nodes, recursively walks the ontology tree until it reaches the root. Collects all visited nodes, which are the ancestors (parents) of the starting nodes.

### Usage

    ancestors(
      terms,
      db_key = "go_basic",
      ids = TRUE,
      relations = c("is_a", "part_of", "occurs_in", "regulates", "positively_regulates",
        "negatively_regulates")
    )

### Arguments

`terms` | Character vector of ontology term IDs or names. A mixture of IDs and names can be provided.
`db_key` | Character: key to identify the ontology database. For the available keys see `omnipath_show_db`.
`ids` | Logical: whether to return IDs or term names.
`relations` | Character vector of ontology relation types. Only these relations will be used.

### Details

Note: this function relies on the database manager, the first call might take long because of the database load process. Subsequent calls within a short period should be faster. See `get_ontology_db`.

### Value

Character vector of ontology IDs. If the input terms are all root nodes, `NULL` is returned. The starting nodes won't be included in the result unless some of them are ancestors of other starting nodes.

### Examples

    ancestors('GO:0005035', ids = FALSE)
    # [1] "molecular_function"
    # [2] "transmembrane signaling receptor activity"
    # [3] "signaling receptor activity"
    # [4] "molecular transducer activity"

[Package OmnipathR version 3.0.0 Index]