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[vds] fix impute_sex_chromosome_ploidy docs #11452

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merged 1 commit into from
Mar 4, 2022

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chrisvittal
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@chrisvittal chrisvittal commented Mar 2, 2022

the actual expression for x/y ploidy is:

    per_sample = coverage.transmute_cols(autosomal_mean_dp=auto_dp,
                                         x_mean_dp=x_dp,
                                         x_ploidy=2 * x_dp / auto_dp,
                                         y_mean_dp=y_dp,
                                         y_ploidy=2 * y_dp / auto_dp)

Comment on lines 374 to 376
- ``x_ploidy`` (*float64*): Estimated ploidy on X chromosome. Equal to ``x_mean_dp / autosomal_mean_dp * 2``.
- ``y_mean_dp`` (*float64*): Mean depth on calling intervals on chromosome.
- ``y_ploidy`` (*float64*): Estimated ploidy on Y chromosome. Equal to ``2 * autosomal_mean_dp / y_mean_dp``.
- ``y_ploidy`` (*float64*): Estimated ploidy on Y chromosome. Equal to ``y_mean_db / autosomal_mean_dp * 2``.
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This associates as (x_mean_dp / autosomal_mean_dp) * 2, right? Could you write it 2 * x_mean_dp / autosomal_mean_dp so there's no ambiguity?

the actual expression for x/y ploidy is:

```python3
    per_sample = coverage.transmute_cols(autosomal_mean_dp=auto_dp,
                                         x_mean_dp=x_dp,
                                         x_ploidy=2 * x_dp / auto_dp,
                                         y_mean_dp=y_dp,
                                         y_ploidy=2 * y_dp / auto_dp)
```
@danking danking merged commit 7f96d4e into hail-is:main Mar 4, 2022
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3 participants