createOntologyNetwork: Create ontology network

In altintasali/ontoClust: Cluster Gene Ontology Terms

Description

Creates a network of ontology terms based on the method provided.

Usage

createOntologyNetwork(
  ontology.id,
  weighted = FALSE,
  method = "jaccard",
  organism = "hsa"
)

Arguments

ontology.id	A character vector of ontology ID from supported ontology databases.
weighted	Weight calculated by method. If FALSE (default), no weight is calculated.
method	Calculated similarity between 2 ontology terms based on the method. Available methods are: jaccard Jaccard Index intersect Number of intersecting genes
organism	Organism identifier (required for GO annotations). Default is "hsa". Currently human (hsa), mouse (mmu) and rat (rno) are supported. Full list of organism IDs can be found [here](https://www.genome.jp/kegg/catalog/org_list.html).

Value

A data.frame with columns:

source

Source node

target

Target node

weight

Weight of edge

Examples

ontology.id <- sample_data$GOBP$ID[1:10]
createOntologyNetwork(ontology.id, method = "jaccard")

altintasali/ontoClust documentation built on Dec. 19, 2021, 1:36 a.m.