preCoreFG {fgga} | R Documentation

## Transitive closure processing of a GO DAG

### Description

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

### Usage

    preCoreFG(myGOnames, domains = "goPlus")

### Arguments

`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")

### Details

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.

### Value

A graphNEL graph with ‘m’ GO node labels.

### 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

### See Also

`fgga2bipartite`

### Examples

    data(CfData)

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

    mygraphGO <- preCoreFG(myGOs, domains = "MF-CC")

[Package fgga version 1.2.0 Index]