wppi_go_data: Retrieves data from Gene Ontology (GO)

In AnaGalhoz37/wppi: Weighting protein-protein interactions

Retrieves data from Gene Ontology (GO)

Description

Gene Ontology (http://geneontology.org/), GO) annotates genes by their function, localization and biological processes.

Usage

wppi_go_data(slim = NULL, aspects = c("C", "F", "P"), organism = "human")

Arguments

slim	Character: use a GO subset (slim). If NULL, the full GO is used. The most often used slim is called "generic". For a list of available slims see OmnipathR::go_annot_slim.
aspects	Character vector with the single letter codes of the gene ontology aspects to use. By default all three aspects are used. The aspects are "C": cellular component, "F": molecular function and "P" biological process.
organism	Character: name of the organism for GO annotations.

Details

If you use a GO subset (slim), building it at the first time might take around 20 minutes. The result is saved into the cache so next time loading the data from there is really quick. Gene Ontology annotations are available for a few other organisms apart from human. The currently supported organisms are "chicken", "cow", "dog", "human", "pig" and "uniprot_all". If you disable HPO_annot you can use wppi to score PPI networks other than human.

Value

A data frame (tibble) with GO annotation data.

See Also

wppi_data

Examples

go <- wppi_go_data()

AnaGalhoz37/wppi documentation built on Nov. 8, 2022, 7:47 a.m.