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gametic heterozygosity_observed #279

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gametic heterozygosity_observed #279

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timothymillar
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@timothymillar timothymillar commented Jul 18, 2019 •
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See #277 for earlier discussion

This updates heterozygosity_observed to use "gametic heterozygosity" which assumes polysomic inheritance (i.e. autopolyploidy).
Gametic heterozygosity is identical to the existing calculation (Nei's method) for the diploid case but generalises it to autopolyploids.

This implementation follows Hardy 2016 and Meirmans and Liu 2018.

An additional argument corrected is added which defaults to True to correct for the ploidy level.
If this is set to False uncorrected Ho is calculated which is discussed in Meirmans and Liu 2018 for comparing across ploidy levels.

Note that the existing code is used as a special case for diploids because it is faster - not because it produces a different result.

I updated the triploid test case though I'm not entirely sure about the applicability to odd-numbered ploidy levels (Edit: this method should be fine for odd ploidy levels).

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pep8speaks commented Jul 18, 2019 •
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Hello @timothymillar! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2020-08-04 07:23:26 UTC

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@alimanfoo I'm having some second thoughts about this PR now.

This heterozygosity_observed still requires a GenotypeArray an hence a single ploidy level for all samples.

If #287 were to be implemented then heterozygosity_observed could be updated for mixed ploidy, but #287 is just a suggestion at this point.

Alternatively a new function could be implemented that takes a GenotypeAlleleCountsArray and assumes the ploidy level at each loci in each sample is equivalent to the sum of allele counts (i.e. it assumes that all genotypes are complete). This would allow for mixed ploidy levels but would require that the user removes any partial genotypes themselves.

@timothymillar
Initial implementation of heterozygosity_individual
6e3dc0f 
This function is based on the definition in Hardy (2016)
"Population genetics of autopolyploids under a mixed mating
model and the estimation of selfing rate".
It calculates the 'level' of heterozygosity of individuals
in a consistant way across ploidy levels such that a diploid
always has a heterozygosity of 0 (hom) or 1 (het) and
a polyploid will always have a values from 0 (fully hom) to
1 (fully het).
@timothymillar
Re-implement heterozygosity_observed using heterozygosity_individual.
65d1412 
This also enables using heterozygosity_observed with mixed-ploidy
data via the 'ploidy' argument.
@timothymillar
Add heterozygosity_individual to init and add tests.
5183488
@timothymillar
Docstring example for heterozygosity_individual
1649eee
@timothymillar
Remove trailing whitespace
7869546
@timothymillar
Docstring
d84e1cb
@timothymillar
Flake8 whitespace
6f6ed5a
@timothymillar
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@alimanfoo I have updated this with the following changes:

  • factored out a heterozygosity_individual function that calculates heterozygosity per individual (0 or 1 for diploids)
  • added a ploidy argument to heterozygosity_individual and heterozygosity_observed to allow for mixed ploidy genotypes (along either/both axes)

I think this is the correct approach for supporting mixed ploidy data as it makes it explicit which functions are supported and avoids complicating the base genotype model.

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@timothymillar @pep8speaks