topo_ic_sim_term: GAPGOM - topo_ic_sim_term()

In Berghopper/GAPGOM: GAPGOM (novel Gene Annotation Prediction and other GO Metrics)

Description

Algorithm to calculate similarity between two GO terms.

Usage

topo_ic_sim_term(organism, ontology, go1, go2, go_data = NULL)

Arguments

organism	where to be scanned genes reside in, this option is neccesary to select the correct GO DAG. Options are based on the org.db bioconductor package; http://www.bioconductor.org/packages/release/BiocViews.html#___OrgDb Following options are available: "fly", "mouse", "rat", "yeast", "zebrafish", "worm", "arabidopsis", "ecolik12", "bovine", "canine", "anopheles", "ecsakai", "chicken", "chimp", "malaria", "rhesus", "pig", "xenopus".
ontology	desired ontology to use for similarity calculations. One of three; "BP" (Biological process), "MF" (Molecular function) or "CC" (Cellular Component).
go1	GO term of first term.
go2	GO term of second term.
go_data	prepared go_data, from the set_go_data function. It is practically the same as in GOSemSim, but with a slightly nicer interface.

Details

This function is made for calculating topological similarity of two GO terms in the GO DAG structure. The topological similarity is based on edge weights and information content (IC). [1]

Value

TopoICSim score between the two terms.

References

[1] Ehsani R, Drablos F: TopoICSim: a new semantic similarity measure based on gene ontology. BMC Bioinformatics 2016, 17(1):296)

Examples

result <- topo_ic_sim_term("human", "MF", "GO:0018478", "GO:0047105")

Berghopper/GAPGOM documentation built on July 2, 2020, 11:57 p.m.