load_genesets_go_bioconductor: Load GO annotations via Bioconductor packages (e.g....

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

Load GO annotations via Bioconductor packages (e.g. org.Hs.eg.db for Human)

Description

Download and import genesets from the GO database using the Bioconductor infrastructure. Use the goat::load_genesets_go_fromfile function for more fine-grained control over the GO database version that you use; it allows you to import NCBI gene2go files

Usage

load_genesets_go_bioconductor(include_child_annotations = TRUE, taxid = 9606)

Arguments

include_child_annotations	boolean; include annotations against child terms? In most situations, TRUE (default) is the desired setting
taxid	integer value that indicates the taxonomy id. Default: 9606 (Human, Homo sapiens). Currently supported options: 9606 = Human (Homo sapiens) 9598 = Chimpanzee (Pan troglodytes) 9544 = Rhesus monkey (Macaca mulatta) 10090 = Mouse (Mus musculus) 10116 = Rat (Rattus norvegicus) 7955 = Zebrafish (Danio rerio) 7227 = Fruit fly (Drosophila melanogaster) 6239 = Worm (Caenorhabditis elegans)

Details

Note that org.Hs.eg.db pulls data semi-annually from NCBI gene2go (as do similar databases for other species), but the GO database version returned by this function is tied to the version of the org.Hs.eg.db on your computer (this is controlled by the Bioconductor infrastructure). E.g. in an outdated R installation you may get outdated GO annotations as well.

The actual GO database version that is retrieved is returned by this function in the source_version column.

Value

table with columns; source (character), source_version (character), id (character), name (character), genes (list), ngenes (int)

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