From 2a266c0ec9efbb95c5bd828fe0dc6eb3325e7b0e Mon Sep 17 00:00:00 2001 From: Shing Zhan Date: Wed, 6 Mar 2024 09:22:52 +0000 Subject: [PATCH] Minor edits to comments --- python/tests/beagle_numba.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/python/tests/beagle_numba.py b/python/tests/beagle_numba.py index f0b2035378..b6f2e8860a 100644 --- a/python/tests/beagle_numba.py +++ b/python/tests/beagle_numba.py @@ -830,7 +830,7 @@ def compute_individual_scores( :return: Genotype probabilities and allele dosages. :rtype: tuple(numpy.ndarray, numpy.ndarray) """ - n = len(alleles_1) # Number of individuals + n = len(alleles_1) # Number of individuals. assert len(alleles_2) == n, "Lengths of alleles differ." assert n > 0, "There must be at least one individual." assert len(allele_probs_1) == n, "Lengths of alleles and probabilities differ." @@ -879,18 +879,18 @@ def compute_allelic_r_squared(gt_probs): :rtype: float """ _MIN_R2_DEN = 1e-8 - n = len(gt_probs) # Number of individuals + n = len(gt_probs) # Number of individuals. assert n > 0, "There must be at least one individual." assert gt_probs.shape[1] == 3, "Three genotypes are considered." f = 1 / n - z = np.argmax(gt_probs, axis=1) # Most likely imputed genotypes + z = np.argmax(gt_probs, axis=1) # Most likely imputed genotypes. u = gt_probs[:, 1] + 2 * gt_probs[:, 2] # E[X | y_i] w = gt_probs[:, 1] + 4 * gt_probs[:, 2] # E[X^2 | y_i] cov = np.sum(z * u) - np.sum(z) * np.sum(u) * f var_best = np.sum(z**2) - np.sum(z) ** 2 * f var_exp = np.sum(w) - np.sum(u) ** 2 * f den = var_best * var_exp - # Minimum of allelic R^2 is zero. See BEAGLE code. + # Minimum of allelic R^2 is zero. allelic_rsq = 0 if den < _MIN_R2_DEN else cov**2 / den return allelic_rsq