preCoreFG {fgga} | R Documentation |
preCoreFG ensures the transitive closure of inference paths -serial concatenation of relationships- in a GO DAG.
preCoreFG(myGOnames, domains = "goPlus")
myGOnames |
A vector with ‘m’ GO node labels |
domains |
A string that indicates which subdomains will be used. Values: “BP-MF", “MF-CC", “BP-CC" or “goPlus" (default, “BP-MF-CC") |
Non-transitive relationships in GO DAG's may lead to non-transitive inference paths precluding the free propagation and consistency checking of GO annotations. A transitive closure screening process over GO DAG's relationships is required before the construction of Forney Factor Graphs. Serial concatenation of relationships leading to non-transitive inference paths in a GO DAG are conformed by removing the most specific relationship.
A graphNEL graph with ‘m’ GO node labels.
Flavio E. Spetale <spetale@cifasis-conicet.gov.ar>
Spetale Flavio E., Arce D., Krsticevic F., Bulacio P. and Tapia E. “Consistent prediction of GO protein localization”. Scientific Report 7787(8), 2018
data(CfData) myGOs <- c(CfData[["nodesGO"]], "GO:1902494", "GO:0032991", "GO:1990234", "GO:0005575") mygraphGO <- preCoreFG(myGOs, domains = "MF-CC")