functional_annot: Functional similarity score based on ontology

In AnaGalhoz37/wppi: Weighting protein-protein interactions

Functional similarity score based on ontology

Description

Functional similarity between two genes in ontology databases (GO or HPO). Each pair of interacting proteins in the PPI graph network, is quantified the shared annotations between them using the Fisher's combined probability test (https://doi.org/10.1007/978-1-4612-4380-9_6). This is based on the number of genes annotated in each shared ontology term and the total amount of unique genes available in the ontology database.

Usage

functional_annot(annot, gene_i, gene_j)

Arguments

annot	Processed annotation data as provided by process_annot.
gene_i	String with the gene symbol in the row of the adjacency matrix.
gene_j	String with the gene symbol in the column of the adjacency matrix.

Value

Numeric value with GO/HPO functional similarity between given pair of proteins.

See Also

• process_annot

• weighted_adj

Examples

hpo <- wppi_hpo_data()
hpo <- process_annot(hpo)
hpo_score <- functional_annot(hpo, 'AKT1', 'MTOR')
# [1] 106.9376

AnaGalhoz37/wppi documentation built on Nov. 8, 2022, 7:47 a.m.