go_obo: simple vectorized parsing of GO OBO file without any...

In goat: Gene Set Analysis Using the Gene Set Ordinal Association Test

simple vectorized parsing of GO OBO file without any dependencies (beyond dplyr/tibble/tidyr)

Description

note that we remove links between GO terms that are across GO domains (e.g. no CC to MF relations) The only supported relations are those that match this regex; "^(is_a:|relationship: part_of|relationship: regulates|relationship: positively_regulates|relationship: negatively_regulates)"

Usage

go_obo(f, rename_namespace = TRUE, remove_obsolete = TRUE)

Arguments

f	full path to go.obo file stored on the computer, e.g. previously downloaded from http://current.geneontology.org/ontology/go.obo . Also works with a gzipped file; obo.gz
rename_namespace	boolean; rename official namespace values like 'cellular_component' to CC? (analogous for BP and MF)
remove_obsolete	boolean; remove obsoleted terms?

Value

tibble with ontology terms and their relations

goat documentation built on April 3, 2025, 6:05 p.m.