walk_ontology_tree: All nodes of a subtree starting from the selected nodes

In saezlab/OmnipathR: OmniPath web service client and more

All nodes of a subtree starting from the selected nodes

Description

Starting from the selected nodes, recursively walks the ontology tree until it reaches either the root or leaf nodes. Collects all visited nodes.

Usage

walk_ontology_tree(
  terms,
  ancestors = TRUE,
  db_key = "go_basic",
  ids = TRUE,
  method = "gra",
  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.
ancestors	Logical: if FALSE the ontology tree is traversed towards the leaf nodes; if TRUE, the tree is traversed until the root. The former returns the ancestors (parents), the latter the descendants (children).
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.
method	Character: either "gra" or "lst". The implementation to use for traversing the ontology tree. The graph based implementation is faster than the list based, the latter will be removed in the future.
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 leaves or roots NULL is returned. The starting nodes won't be included in the result unless they fall onto the traversal path from other nodes.

See Also

• omnipath_show_db

• get_ontology_db

Examples

walk_ontology_tree(c('GO:0006241', 'GO:0044211'))
# [1] "GO:0006139" "GO:0006220" "GO:0006221" "GO:0006241" "GO:0006725"
# [6] "GO:0006753" "GO:0006793" "GO:0006796" "GO:0006807" "GO:0008150"
# ... (truncated)
walk_ontology_tree(c('GO:0006241', 'GO:0044211'), ancestors = FALSE)
# [1] "GO:0044210" "GO:0044211"
walk_ontology_tree(
    c('GO:0006241', 'GO:0044211'),
    ancestors = FALSE,
    ids = FALSE
)
# [1] "'de novo' CTP biosynthetic process" "CTP salvage"

saezlab/OmnipathR documentation built on Nov. 10, 2024, 11:02 p.m.