limix.qc.indep_pairwise¶
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limix.qc.
indep_pairwise
(X, window_size, step_size, threshold, verbose=True)[source]¶ Determine pair-wise independent variants.
Independent variants are defined via squared Pearson correlations between pairs of variants inside a sliding window.
Parameters: - X (array_like) – Sample by variants matrix.
- window_size (int) – Number of variants inside each window.
- step_size (int) – Number of variants the sliding window skips.
- threshold (float) – Squared Pearson correlation threshold for independence.
- verbose (bool) – True for progress information; False otherwise.
Returns: ok
Return type: boolean array defining independent variants
Examples
>>> from numpy.random import RandomState >>> from limix.qc import indep_pairwise >>> >>> random = RandomState(0) >>> X = random.randn(10, 20) >>> >>> indep_pairwise(X, 4, 2, 0.5, verbose=False) array([ True, True, False, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True])