process_annot {wppi} | R Documentation |
Ontology databases such as Gene Ontology (GO, http://geneontology.org/) and Human Phenotype Ontology (HPO, https://hpo.jax.org/app/) provide important genome and disease functional annotations of genes. These combined allow to build a connection between proteins/genes and phenotype/disease. This function aggregates information in the GO and HPO ontology datasets.
process_annot(data_annot)
data_annot |
Data frame (tibble) of GO or HPO datasets from
|
A list of four elements: 1) "term_size" a list which serves as a
lookup table for size (number of genes) for each ontology term; 2)
"gene_term" a list to look up terms by gene symbol; 3) "annot" the
original data frame (data_annot
); 4) "total_genes" the number of
genes annotated in the ontology dataset.
hpo_raw <- wppi_hpo_data() hpo <- process_annot(hpo_raw)