INNER CODE UNIT · Python
depth
wheaton5/souporcell · compile_stan_model.py:52
depth = cluster_allele_counts_soup[locus][cluster][1] + cluster_allele_counts_soup[locus][cluster][2];
if (depth == 0) {
continue;
}
p_hom_ref = (1.0 - p_soup) * 1.0 + p_soup * average_allele_expression_soup[locus][1]/(average_allele_expression_soup[locus][1] + average_allele_expression_soup[locus][2]);
p_hom_alt = (1.0 - p_soup) * 1.0 + p_soup * average_allele_expression_soup[locus][2]/(average_allele_expression_soup[locus][1] + average_allele_expression_soup[locus][2]);
p_het_ref = (1.0 - p_soup) * 0.5 + p_soup * average_allele_expression_soup[locus][1]/(average_allele_expression_soup[locus][1] + average_allele_expression_soup[locus][2]);
p_err = average_allele_expression_soup[locus][1]/(average_allele_expression_soup[locus][1] + average_allele_expression_soup[locus][2]);
hom_ref = binomial_lpmf(cluster_allele_counts_soup[locus][cluster][1] | depth, p_hom_ref);
hom_alt = binomial_lpmf(cluster_allele_counts_soup[locus][cluster][2] | depth, p_hom_alt);
het = binomial_lpmf(cluster_allele_counts_soup[locus][cluster][1] | depth, p_het_ref);
err += binomial_lpmf(cluster_allele_counts_soup[locus][cluster][1] | depth, p_err);
stuff[1] = hom_ref + neg_log_3;