validate_associations_mkg: Validate associations with the Monarch Knowledge Graph

View source: R/validate_associations_mkg.R

validate_associations_mkgR Documentation

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.