process_annot: Processing of ontology annotations

In AnaGalhoz37/wppi: Weighting protein-protein interactions

Processing of ontology annotations

Description

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.

Usage

process_annot(data_annot)

Arguments

data_annot

Data frame (tibble) of GO or HPO datasets from wppi_data, wppi_go_data or wppi_hpo_data.

Value

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.

See Also

• wppi_data

• wppi_go_data

• wppi_hpo_data

Examples

hpo_raw <- wppi_hpo_data()
hpo <- process_annot(hpo_raw)

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