dot-topo_ic_sim_geneset: GAPGOM internal - .topo_ic_sim()

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_geneset(gene_list1, gene_list2, topoargs)

Arguments

gene_list1	The first gene vector of gene IDs. Note; THIS IS NOT THE ENSEMBLID. Instead use the gene ID adopted by NCBI.
gene_list2	Same type as gene_list1, will be compared to gene_list1.
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 two gene vectors. This function is made for calculating topological similarity between two gene lists of which each gene has its GO terms in the GO DAG structure. The topological similarity is based on edge weights and information content (IC). The output it a nxn matrix depending on the vector lengths. Intraset similarity can be calculated by comparing the same gene vector to itself and using mean() on the output. The same can be done for Interset similarity, but between two different gene lists. [1]

Value

List containing the following; $GeneSim; similarity between genes taken from the mean of all term similarities within those genes. (matrix of similarities between genes). Take the mean of this matrix to either get the InterSetSim or IntraSetSim depending on your input. $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.