Cohort subsets #394
Cohort subsets #394
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tomwhite
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I've now run this successfully on the MalariaGEN data: H stats: https://nbviewer.jupyter.org/github/tomwhite/shiny-train/blob/sgkit/notebooks/gwss/sgkit_h12.ipynb Example usage: |
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This is powerful stuff, thanks @tomwhite! A minor comment above, merge away as you see fit.
sgkit/cohorts.py
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| Returns | ||
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| An array of shape ``(len(cohorts), tuple_len)``, where ``tuple_len`` is the length | ||
| of the tuples, or 1 if ``cohorts`` is a sequence of values., |
| tuples to an array of ints used to match samples in ``sample_cohorts``. | ||
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| Cohorts can be specified by index (as used in ``sample_cohorts``), or a label, in | ||
| which case an ``index`` must be provided to find index locations for cohorts. |
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Any chance of a couple of simple examples here and the return values? I'm finding it a bit abstract and a concrete example would help understand what the function does.
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Thanks for the review @jeromekelleher. Added two examples in pystatgen/sgkit@f4b45ea
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Codecov Report
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This addresses https://github.com/pystatgen/sgkit/issues/224#issuecomment-694350208 for specifying cohort subsets (for Garud H and PBS).
This is a draft since I haven't run it on MalariaGEN scale data yet, but I'd welcome any initial feedback.