go_obo

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;
<code>"^(is_a:|relationship: part_of|relationship: regulates|relationship: positively_regulates|relationship: negatively_regulates)"</code>

Perform gene set enrichment analyses using the Gene set Ordinal
Association Test (GOAT) algorithm and visualize your
results. Koopmans, F. (2024) <doi:10.1038/s42003-024-06454-5>.

Frank Koopmans

goat

Gene Set Analysis Using the Gene Set Ordinal Association Test

go_obo function

<dl><dt>f</dt>
<dd>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</dd>
<dt>rename_namespace</dt>
<dd>boolean; rename official namespace values like 'cellular_component' to CC? (analogous for BP and MF)</dd>
<dt>remove_obsolete</dt>
<dd>boolean; remove obsoleted terms?</dd></dl>

Arguments

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

<dl>

<dt>f</dt>
<dd>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</dd>


<dt>rename_namespace</dt>
<dd>boolean; rename official namespace values like 'cellular_component' to CC? (analogous for BP and MF)</dd>


<dt>remove_obsolete</dt>
<dd>boolean; remove obsoleted terms?</dd>

</dl>

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

Description

Usage

Value

Arguments