preCoreFG: Transitive closure processing of a cross-ontology DAG
In fspetale/fgga: Hierarchical ensemble method based on factor graph

preCoreFG

R Documentation

Transitive closure processing of a cross-ontology DAG

Description

preCoreFG ensures the transitive closure of inference paths -serial concatenation of relationships- in a cross-ontology DAG.

Usage

preCoreFG(ontoTerms, domains = "GO")

Arguments

`ontoTerms`	A vector with ‘m’ cross-ontology node labels
`domains`	A string that indicates which subdomains or ontologies will be used. Values: “GOBP", “GOMF", “GOCC", “GOCC-PO", “GOCC-ZFA", “GOBP-HPO", “GOMF-HPO", “GOCC-HPO", “GO-PO", “GO-ZFA", “GO-HPO", “GO" (default, “BP-MF-CC")

Details

Non-transitive relationships in cross-ontology DAG's may lead to non-transitive inference paths precluding the free propagation and consistency checking of ontology annotations. A transitive closure screening process over cross-ontology DAG's relationships is required before the construction of Forney Factor Graphs. Serial concatenation of relationships leading to non-transitive inference paths in a cross-ontology DAG are conformed by removing the most specific relationship.

Value

A graphNEL graph with ‘m’ node labels belong to ontologies used.

Author(s)

Flavio E. Spetale <spetale@cifasis-conicet.gov.ar>

References

Spetale Flavio E., Arce D., Krsticevic F., Bulacio P. and Tapia E. “Consistent prediction of GO protein localization”. Scientific Report 7787(8), 2018

Examples


data(CfData)

myGOs <- c(CfData[["nodesGO"]], "GO:1902494", "GO:0032991", "GO:1990234",
            "GO:0005575")


# mygraphGO <- preCoreFG(myGOs, domains = "GOMF")

fspetale/fgga documentation built on Jan. 29, 2024, 6:53 p.m.