genophenocorr 0.1.0

Search for genotype-phenotype correlations with GA4GH phenopackets

Genophenocorr is a Python library for genotype-phenotype association analysis.

An example of simple genotype-phenotype association analysis

# Load HPO
import hpotk
hpo = hpotk.load_minimal_ontology('http://purl.obolibrary.org/obo/hp.json')

# Load a cohort of phenopackets 
from genophenocorr.data import get_toy_cohort
cohort = get_toy_cohort()

# Analyze genotype-phenotype associations 
from genophenocorr.analysis import CohortAnalysis
from genophenocorr.constants import VariantEffect

cohort_analysis = CohortAnalysis(cohort, 'NM_1234.5', hpo)
frameshift = cohort_analysis.compare_by_variant_type(VariantEffect.FRAMESHIFT_VARIANT)
print(frameshift)

prints a table with genotype-phenotype correlations:

                            With frameshift_variant         Without frameshift_variant
                                              Count Percent                      Count Percent  p-value
HP:0001166 (Arachnodactyly)                       4  30.77%                         10  76.92%  0.04718
HP:0001250 (Seizure)                             11  84.62%                          9  69.23%  0.64472
HP:0001257 (Spasticity)                           8  61.54%                          9  69.23%  1.00000

Documentation

Check out the User guide and the API reference for more info:

• Stable documentation (last release on main branch)
• Latest documentation (bleeding edge, latest commit on development branch)