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

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

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,
  gene_ids = NULL,
  keytype = "ensembl",
  columns = c("go", "goall", "goid")
)

Arguments

orgdb	OrganismDb instance.
gene_ids	Identifiers of the genes to retrieve annotations.
keytype	The mysterious keytype returns yet again to haunt my dreams.
columns	The set of columns to request.

Details

Tested in test_45ann_organdb.R 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]

Examples

 drosophila_orgdb_go <- load_orgdb_go(orgdb = "org.Dm.eg.db")
 head(drosophila_orgdb_go)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.