subset_phenos: Subset RD EWCE results

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

Subset RD EWCE results

Description

This subsets the Rare disease EWCE results by cell type, q threshold and fold change.

Usage

subset_phenos(
  filters = NULL,
  keep_descendants = NULL,
  results = load_example_results(),
  hpo = HPOExplorer::get_hpo(),
  q_threshold = 5e-04,
  effect_threshold = 1,
  verbose = TRUE
)

Arguments

filters	A named list, where each element in the list is the name of a column in the data, and the vector within each element represents the values to include in the final data.
keep_descendants	Terms whose descendants should be kept (including themselves). Set to NULL (default) to skip this filtering step.
results	The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results
hpo	Human Phenotype Ontology object, loaded from get_ontology.
q_threshold	The q value threshold to subset the results by.
effect_threshold	The minimum fold change in specific expression to subset the results by.
verbose	Print messages.

Value

A data frame of results taken from the main data frame of results.

Examples

phenos <- subset_phenos(filters = list(CellType = "Cardiomyocytes"),
                        keep_descendants = "Neurodevelopmental delay")

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