validate_associations_mkg: Validate associations with the Monarch Knowledge Graph

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

Validate associations with the Monarch Knowledge Graph

Description

This function validates the associations between phenotypes and cell types with the Monarch Knowledge Graph (MKG). It computes the number of phenotypes and cell types that are present in the MKG and the number of associations that are present in the MKG.

Usage

validate_associations_mkg(
  results = load_example_results(),
  kg = get_data("monarch_kg_cells.csv"),
  q_threshold = 0.05,
  cl = KGExplorer::get_ontology(name = "cl", remove_cyclic_paths = TRUE, remove_rings =
    TRUE),
  alt_ids = c(`CL:0000111` = "CL:2000032"),
  metric = c("dist_nca.min_adj", "dist_lca.min_adj", "dist_nca.min", "dist_lca.min")[1]
)

Arguments

results	The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results
kg	A data.table with phenotype-cell type relationships ("from" and "to" columns, respectively) gathered from the Monarch Knowledge Graph.
q_threshold	The q value threshold to subset the results by.
cl	Cell Ontology object.
alt_ids	Alternative IDs to map CL IDs into.
metric	Ontological distance metric to use for plotting.

Examples

results <- load_example_results()
kg <- validate_associations_mkg(result=results)

neurogenomics/MultiEWCE documentation built on Sept. 28, 2024, 2:27 a.m.