gpsea.analysis.pscore.stats package

class gpsea.analysis.pscore.stats.PhenotypeScoreStatistic(name: str)[source]

Bases: Statistic

PhenotypeScoreStatistic calculates a p value for 2 or more phenotype score groups computed by a PhenotypeScorer.

abstract compute_pval(scores: Collection[Sequence[float]]) → float[source]
class gpsea.analysis.pscore.stats.MannWhitneyStatistic[source]

Bases: PhenotypeScoreStatistic

MannWhitneyStatistic is a wrapper around SciPy’s mannwhitneyu() function to apply Mann-Whitney U rank test on 2 phenotype scores.

The NaN phenotype score values are ignored.

See Compare phenotype scores in genotype groups for an example usage.

compute_pval(scores: Collection[Sequence[float]]) → float[source]
class gpsea.analysis.pscore.stats.TTestStatistic[source]

Bases: PhenotypeScoreStatistic

TTestStatistic is a wrapper around SciPy’s ttest_ind() function to apply T test on 2 phenotype scores.

The NaN phenotype score values are ignored.

compute_pval(scores: Collection[Sequence[float]]) → float[source]