dot-topo_ic_sim_g1g2: GAPGOM internal - .topo_ic_sim_g1g2()

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

Description

This function is an internal function and should not be called by the user.

Usage

.topo_ic_sim_g1g2(gene1, gene2, topoargs)

Arguments

gene1	Gene ID of the first Gene.
gene2	Gene ID of the second Gene.
topoargs	list containing all the neccesary paramters/arguments for the topoicsim algorithm, details can be view in the ".prepare_variables_topoicsim" function.

Details

Algorithm to calculate similarity between GO terms of two genes. This function is made for calculating topological similarity of two Genes given their GO terms in the GO DAG structure. The topological similarity is based on edge weights and information content (IC). [1]

Value

List containing the following; $GeneSim; similarity between genes taken from the mean of all term similarities. $AllGoPairs; All possible GO combinations with their semantic distances (matrix)

Notes

Internal function used in (topo_ic_sim_genes()).

References

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

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