load_genesets_go_bioconductor {goat} | R Documentation |
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:
|
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 E.g. in an outdated R installation you may get outdated GO annotations as well.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)