fgga2bipartite: Forney Factor Graph model

In fspetale/fgga: Hierarchical ensemble method based on factor graph

Forney Factor Graph model

Description

fgga2bipartite builds a Forney Factor Graph from a FGGA model.

Usage

fgga2bipartite(graphOnto)

Arguments

graphOnto

A graphNEL graph with ‘m’ cross-Ontology node labels.

Details

The Gene Ontology (GO) is structured as a directed acyclic graph (DAG) with nodes (GO-terms) representing gene functions and edges characterizing relationships between nodes. A variety of relationships are possible (currently 8). To compute GO-term predictions perfectly aware of GO-term relationships, a Forney Factor Graph is required. Hence, GO-terms are mapped to binary variable nodes, and relationships to logical factor nodes.

Value

A binary matrix with 2*m rows by 2*m-1 columns where m is the quantity of cross-Ontology node labels.

Author(s)

Flavio E. Spetale <[e-mail]>

References

F. Spetale, J. Murillo, E. Tapia, D. Arce, S. Ponce, and P. Bulacio, “Formal modeling of gene ontology annotation predictions based on factor graphs,” Journal of Physics: Conference Series, vol. 705, no. 1, p. 012001, 2016.

Spetale F.E., Tapia E., Krsticevic F., Roda F. and Bulacio P. “A Factor Graph Approach to Automated GO Annotation”. PLoS ONE 11(1): e0146986, 2016.

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)

graphGO <- as(CfData$graphCfGO, "graphNEL")
fgga2bipartite(graphGO)

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