Update docstring

python/tests/beagle_numba.py

@@ -681,9 +681,9 @@ def compute_individual_scores(alleles_1, allele_probs_1, alleles_2, allele_probs
 # Site-level data.
 def compute_estimated_allelic_r_squared(gt_probs):
     """
-    Compute the estimated allelic R^2 for an imputed site.
+    Compute the estimated allelic R^2 at a site from posterior genotype probabilities.
 
-    Assume that all sites are biallelic. Otherwise, the calculation below is incorrect.
+    Assume that site is biallelic. Otherwise, the calculation below is incorrect.
     Note that 0 refers to the major allele and 1 the minor allele.
 
     It is not the true allelic R^2, which needs access to true genotypes to compute.
@@ -693,7 +693,7 @@ def compute_estimated_allelic_r_squared(gt_probs):
     In BEAGLE 4.1, it is AR2: "Allelic R-Squared: estimated squared correlation
     between most probable REF dose and true REF dose".
 
-    See formulation in the Appendix 1 of Browning and Browning. (2009).
+    See the formulation in the Appendix 1 of Browning & Browning (2009).
     Am J Hum Genet. 84(2): 210–223. doi: 10.1016/j.ajhg.2009.01.005.
 
     :param numpy.ndarray alleles_1: Imputed alleles for haplotype 1.
@@ -725,9 +725,10 @@ def compute_dosage_r_squared():
 
 def compute_allele_frequency(gt_probs, allele=1):
     """
-    Estimate allele frequencies from posterior genotype probabilities.
+    Estimate the frequency of an allele at a site from posterior genotype probabilities.
 
-    Assume the site is biallelic. 0 denotes the major allele, and 1 the minor allele.
+    Assume that site is biallelic. Otherwise, the calculation below is incorrect.
+    Note that 0 refers to the major allele and 1 the minor allele.
 
     Input are the posterior genotype probabilities at a site for n diploid individuals:
     P(00), P(01 or 10), and P(11). The matrix is of size (n, 3).