Tutorial

ppkt2synergy allws users to perform both correlation and synergy analyis (TODO explanations!). We recommend the use of Jupyter notebooks to perform the analysis, but one could also use a Python script.

Correlation analysis

First, we import the necessary packages. (Explain phenopacket store). The name of the cohort should be the same as that used in phenopacket store.

from ppkt2synergy import CohortDataLoader, HPOStatisticsAnalyzer, PhenopacketMatrixProcessor, CorrelationType
from ppkt2synergy import __version__
cohort_name = "CTCF"
phenopackets = CohortDataLoader.from_ppkt_store(cohort_name=cohort_name)
print(f"[ppkt2synergy] version {__version__} loaded")
print(f"n={len(phenopackets)} phenopackets from {cohort_name} cohort.")

Ingest the HPO data

The library creates a matrix of HPO co-occurences.

hpo_matrix, _ = PhenopacketMatrixProcessor.prepare_hpo_data(
    phenopackets=phenopackets, 
    threshold=0, 
    mode=None, 
    use_label=True,
    nan_strategy=None)