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monarch-initiative / genophenocorr

Genotype Phenotype Correlation
https://monarch-initiative.github.io/genophenocorr/stable
MIT License
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compare #9

Closed pnrobinson closed 1 year ago

pnrobinson commented 1 year ago

@lnrekerle

RunStats -- this could probably just be a method in Cohort also do not print from within the method if we are returning a data frame

The following variable names are not quite correct, because I think we are just looking at observed HPOs

all_hpo = PatientList.list_all_phenotypes()

should be

all_observed_hpo_ids = PatientList.get_observed_HPO_id_list()

lnrekerle commented 1 year ago

Moved run_stats to cohort and moved "has_hpo" to patient. Renamed all_hpo to hpo_ids_to_compare since it is now removing all hpo_ids that are not present in at least 10% of patients, so it's no longer "all observed" ids.