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eric-czech opened this issue Jul 8, 2020 · 1 comment
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Add HWE test implementation #28

eric-czech opened this issue Jul 8, 2020 · 1 comment
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@eric-czech
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core operations Issues related to domain-specific functionality such as LD pruning, PCA, association testing, etc. enhancement New feature or request

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This is a somewhat critical function for UKB GWAS and a very important one for pipelines that start further upstream.

The API as I have it sketched out in stats/hwe.py works by taking a dataset and producing a dataset with a single variable:

call_genotype = simulate_genotype_calls(...)
ds = to_genotype_call_dataset(call_genotype)
p = sgkit.hardy_weinberg_test(ds)["variant/hwe_p_value"]

This is currently blocked by https://github.com/pystatgen/sgkit/pull/16 and to some extent https://github.com/pystatgen/sgkit/issues/3.
@eric-czech eric-czech self-assigned this Jul 8, 2020
@eric-czech eric-czech mentioned this issue Jul 8, 2020
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@eric-czech eric-czech added the enhancement New feature or request label Jul 9, 2020
@hammer hammer added the core operations Issues related to domain-specific functionality such as LD pruning, PCA, association testing, etc. label Jul 9, 2020
This was referenced Jul 24, 2020
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@eric-czech eric-czech mentioned this issue Aug 17, 2020
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@eric-czech
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Done in https://github.com/pystatgen/sgkit/pull/76

This was referenced Aug 27, 2020
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