Replaced pooled global Aes with population average Aes #155
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standage
commented
Sep 25, 2024
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| agg_tallies = defaultdict(Counter) | ||
| for n, row in haplotypes.iterrows(): | ||
| for haplokey in ("Haplotype1", "Haplotype2"): | ||
| mhallele = [row[haplokey]] | ||
| if not pd.isna(mhallele): | ||
| # The following line could arguably be moved into the conditional block below to | ||
| # excluded admixed individuals from the aggregate haplotype tallies. But as of | ||
| # today, I think including them in the aggregate totals is appropriate. | ||
| # -- DSS, 2023-02-28. | ||
| agg_tallies[row["Marker"]].update(mhallele) | ||
| pop_tallies[row["Marker"]][row["Population"]].update(mhallele) | ||
| if row["Population"] not in admixed: | ||
| pop_tallies[row["Marker"]][row["Superpopulation"]].update(mhallele) | ||
| for marker, popcounts in sorted(pop_tallies.items()): | ||
| total_count = sum(agg_tallies[marker].values()) | ||
| for mhallele, agg_count in sorted(agg_tallies[marker].items()): | ||
| freq = agg_count / total_count | ||
| yield marker, "1KGP", mhallele, freq, total_count |
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No need to calculate pooled frequencies any more.
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| superpops = ("AFR", "AMR", "EAS", "EUR", "SAS") | ||
| for marker, marker_data in frequencies.groupby("Marker"): | ||
| population_aes = list() | ||
| for population, pop_data in marker_data.groupby("Population"): | ||
| ae = 1.0 / sum([f**2 for f in pop_data.Frequency]) | ||
| entry = (marker, population, ae) | ||
| aes.append(entry) | ||
| if population not in superpops: | ||
| population_aes.append(ae) | ||
| avg_ae = sum(population_aes) / len(population_aes) | ||
| entry = (marker, "1KGP", avg_ae) | ||
| aes.append(entry) |
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Instead, we average population-level Ae values here.
added 2 commits
September 25, 2024 13:54
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The default Ae values currently in MicroHapDB are calculated from a pool of all observed haplotypes in the entire global 26-population data set. This PR changes the build process so that the default values are computed as the mean of the 26 population-specific Ae values, rather than from the entire pool.