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test_val_trend_entropy

Function

crisgi.test_val_trend_entropy(
    interactions,
    method="prod",
    p_cutoff=0.05,
    out_prefix="./test",
)

Performs trend and zero-trend statistical tests on a list of interactions using entropy-based values, identifying validation trend expressed interactions (TERs) based on significance thresholds.

Parameters

Name Type Description
interactions list of str List of interaction names to be tested.
method str, optional Correlation method used for entropy calculation. Default is 'prod'.
p_cutoff float, optional Significance threshold for trend and zero-trend tests. Default is 0.05.
out_prefix str, optional Prefix for the output CSV file containing TER statistics. Default is './test'.

Return type

list of str

Returns

A list of interaction names that are identified as validation trend expressed interactions (TERs) based on the specified statistical criteria.

Attributes Set

  • Saves a CSV file named {out_prefix}_TER.csv containing the trend and zero-trend test results for all tested interactions.

Example

# Assume `crisgi` is an instance of the CRISGI class and edata is already set up.

interactions = ['geneA', 'geneB', 'geneC']
candidates = crisgi.test_val_trend_entropy(
    interactions=interactions,
    method='prod',
    p_cutoff=0.01,
    out_prefix='./results/val_trend'
)

print("TER candidates:", candidates)
# Output CSV will be saved as './results/val_trend_TER.csv'