KGBN.phenotype_score

Functions for listing packaged phenotypes, selecting ProxPath gene-phenotype relationships, and computing phenotype scores from simulated steady-state results.

KGBN.phenotype_score.get_phenotypes(file_path=PosixPath('/home/runner/work/KGBN/KGBN/src/KGBN/data/significant_paths_to_phenotypes.txt'))

KGBN.phenotype_score.proxpath(genes, phenotypes=['APOPTOSIS', 'DIFFERENTIATION', 'PROLIFERATION'], file_path=PosixPath('/home/runner/work/KGBN/KGBN/src/KGBN/data/significant_paths_to_phenotypes.txt'))

This function is used to get the phenotype score for a given list of genes and phenotypes using ProxPath. Args:

genes: list of genes phenotypes: list of phenotypes file_path: path to the ProxPath file

Returns:

pheno_df: dataframe with the phenotype score

KGBN.phenotype_score.phenotype_scores(phenotypes=['APOPTOSIS', 'DIFFERENTIATION', 'PROLIFERATION'], file_path=PosixPath('/home/runner/work/KGBN/KGBN/src/KGBN/data/significant_paths_to_phenotypes.txt'), genes=None, simulation_results=None, network=None, reversed=False)

Calculate phenotype scores for given genes and phenotypes using ProxPath. If simulation_results is not provided, it will return the formula to calculate the score. Otherwise, it will return the phenotype score directly as a DataFrame.