tableTPG {fgga}R Documentation

Valid configurations for hidden variable nodes in a Forney Factor Graph

Description

tableTPG provides valid configurations of hidden variable nodes at logical function nodes in a Forney Factor Graph under the True Path Graph (TPG) constraint.

Usage

tableTPG(att)

Arguments

att

An integer indicating the number of GO nodes involved

Details

Valid configurations of hidden variable nodes at logical function nodes enable messaging passing across the Forney Factor Graph. The TPG constraint is defined as: “If the child GO node describes the protein, then all its parent terms must also apply to that protein; and if a GO node does not describe a protein, then all its descendant GO nodes must not describe it”. The TPG constraint governs the structure of the GO-DAG and the inference process in the associated Forney Factor Graph.

Value

A binary matrix with (n-1)^2+1 rows by n+1 columns where n = attr

Author(s)

Flavio E. Spetale, Pilar Bulacio and Javier Murillo <spetale@cifasis-conicet.gov.ar>

References

Tanoue J, Yoshikawa M, Uemura S (2012). The Gene Around GO viewer. Bioinformatics 18(12): 1705–1706.

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

Examples

tableTPG(3)

[Package fgga version 1.1.0 Index]