load_orgdb_go: Retrieve GO terms associated with a set of genes.

In khughitt/EuPathDB: Provides access to pathogen annotation resources available on EuPathDB databases

Retrieve GO terms associated with a set of genes.

Description

AnnotationDbi provides a reasonably complete set of GO mappings between gene ID and ontologies. This will extract that table for a given set of gene IDs.

Usage

load_orgdb_go(orgdb = NULL)

Arguments

orgdb

OrganismDb instance.

Details

This is a nice way to extract GO data primarily because the Orgdb data sets are extremely fast and flexible, thus by changing the keytype argument, one may use a lot of different ID types and still score some useful ontology data.

Value

Data frame of gene IDs, go terms, and names.

Author(s)

I think Keith provided the initial implementation of this, but atb messed with it pretty extensively.

See Also

AnnotationDbi GO.db magrittr select tbl_df

Examples

## Not run: 
 go_terms <- load_go_terms(org, c("a","b"))

## End(Not run)

khughitt/EuPathDB documentation built on Nov. 4, 2023, 4:19 a.m.