This subsets the Rare disease EWCE results by cell type, q threshold and fold change.
subset_phenos(
cell_type,
ancestor = NULL,
results = load_example_results(),
hpo = HPOExplorer::get_hpo(),
phenotype_to_genes = HPOExplorer::load_phenotype_to_genes(),
q_threshold = 5e-04,
fold_threshold = 1,
verbose = TRUE
)The cell type of interest to be plotted.
Can be a single string (e.g. "Astrocytes") or a character vector
of multiple cell types (e..g. c("Astrocytes","Microglia")).
Set to NULL if you wish to include all cell-types that are available
(after q_threshold and fold_threshold filtering).
If >1 cell-type remains, results will be aggregated automatically
such that there is only 1 node per phenotype.
The ancestor to get all descendants of. If NULL,
returns the entirely ontology.
The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results.
Human Phenotype Ontology object, loaded from ontologyIndex.
Output of load_phenotype_to_genes mapping phenotypes to gene annotations.
The q value threshold to subset the results by.
The minimum fold change in specific expression
to subset the results by.
Print messages.
A data frame of results taken from the main data frame of results.
phenos <- subset_phenos(cell_type = "Amacrine cells",
ancestor = "Neurodevelopmental delay")
#> Subsetting results by q_threshold and fold_change.
#> WARNING!: CellType 'Amacrine cells' ... not found in results.
#> Defaulting to first CellType available: 'ENS_glia'
#> 22,444 associations remain after filtering.
#> Subsetting phenotypes to only ancestors of: Neurodevelopmental delay
#> Translating all phenotypes to HPO IDs.
#> ℹ All local files already up-to-date!
#> + Returning a vector of phenotypes (same order as input).
#> 453 associations remain after filtering.