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monarch-initiative / genophenocorr

Genotype Phenotype Correlation
https://monarch-initiative.github.io/genophenocorr/stable
MIT License
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hpotk #14

Closed pnrobinson closed 11 months ago

pnrobinson commented 1 year ago

@ielis @lnrekerle we should use the hpo-toolkit library for genophenocorr as well. https://github.com/TheJacksonLaboratory/hpo-toolkit

We should check that all HPO terms in our input are valid We should use hpotk also to get all ancestor terms. When we are iterating over HPO terms to do the Fisher exact test, we should check whether any of the child terms has the same counts (if so, we do not need to do the test!)

lnrekerle commented 1 year ago

@pnrobinson

I have started working on that! I have hpotk being used to validate HPO terms in the phenotype class, and I created a function that groups all connected HPO terms together and tests them all at once.

For example, Generalized-onset seizure, Seizure, Generalized myoclonic seizure, and Generalized non-motor (absence) seizure would all be counted as Seizure since all the others are descendants of Seizure.

pnrobinson commented 1 year ago

sounds good -- let's take a look at that with @ielis next week to optimize!

ielis commented 11 months ago

I think this has been addressed..