def calculate_ld_stats(snp1, snp2, samples=None):
calls1 = choose_samples(snp1.record, sample_names=samples)
calls2 = choose_samples(snp2.record, sample_names=samples)
haplo_counts = _count_biallelic_haplotypes(calls1, calls2)
fisher = _fisher_exact(haplo_counts)
rsqr = _calculate_r_sqr(haplo_counts)
return LDStats(fisher, rsqr)
def calculate_r_sqr(snp1, snp2, samples=None):
calls1 = choose_samples(snp1.record, sample_names=samples)
calls2 = choose_samples(snp2.record, sample_names=samples)
haplo_counts = _count_biallelic_haplotypes(calls1, calls2)
if haplo_counts is None:
return None
return _calculate_r_sqr(haplo_counts)
def fisher_exact(snp1, snp2, samples=None):
calls1 = choose_samples(snp1.record, sample_names=samples)
calls2 = choose_samples(snp2.record, sample_names=samples)
haplo_counts = _count_biallelic_haplotypes(calls1, calls2)
return _fisher_exact(haplo_counts)