Add dynamic chisq-based r2 threshold - Githubissues

FINNGEN / autoreporting

MIT License

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Add dynamic chisq-based r2 threshold #172

Closed Lipastomies closed 3 years ago

Lipastomies commented 3 years ago

closes #170

Adds argument --dynamic-r2-chisq (mutually exclusive with --ld-r2), wich can be used in two ways:

With only --dynamic-r2-chisq, r2 threshold is calculated with r2*chi2.isf(pval-df=1) = 5
With --dynamic-r2-chisq VALUE the r2 threshold is calculated with r2*chi2.isf(pval-df=1) = VALUE

Also updated dockerfile &requirements file to use scipy