GetDAG: Organism-specific GO-DAG edgelist

In GOxploreR: Structural Exploration of the Gene Ontology (GO) Knowledge Base

Organism-specific GO-DAG edgelist

Description

Derive the organism gene association GO-terms as an edgelist. It indicates how the terms are linked together. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish","Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", " Escherichia coli / E.coli"

Usage

GetDAG(organism, domain = "BP")

Arguments

organism	An object of class character that represents the organism. If the organism option is "BP", "MF" or "CC" the biological process, molecular function and cellular component general GO edgelist are obtained respectively
domain	The ontology of the GO-terms. The default is BP.

Value

A two-column matrix of the nodes and the edges to which they are connected

Examples

# Edgelist for entire GO BP ontology

GetDAG(organism = "BP")

# Edgelist for cellular component gene association GO-terms for organism Yeast
GetDAG(organism = "Yeast", domain = "CC")

# Edgelist for molecular function gene association GO-terms for organism Zebrafish
GetDAG(organism = "Zebrafish", domain = "MF")

GOxploreR documentation built on Nov. 3, 2023, 5:08 p.m.