functional_annot {wppi} | R Documentation |
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.
functional_annot(annot, gene_i, gene_j)
annot |
Processed annotation data as provided by
|
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. |
Numeric value with GO/HPO functional similarity between given pair of proteins.
hpo <- wppi_hpo_data() hpo <- process_annot(hpo) hpo_score <- functional_annot(hpo, 'AKT1', 'MTOR') # [1] 106.9376