Subset RD EWCE results

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

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")
#> Subsetting results by q_threshold and effect.
#> Selected CellType : 
#>  - Cardiomyocytes
#> Filtered 'CellType' : 1,204 / 1,230 rows dropped.
#> 26 associations remain after filtering.
#> Translating ontology terms to ids.
#> Keeping descendants of 1 term(s).
#> 30 terms remain after filtering.
#> 0 associations remain after filtering.