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Feature request: Automatically collapse ultra-rare variants #32

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dvg-p4 opened this issue Dec 4, 2024 · 0 comments
Open

Feature request: Automatically collapse ultra-rare variants #32

dvg-p4 opened this issue Dec 4, 2024 · 0 comments

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@dvg-p4
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dvg-p4 commented Dec 4, 2024

In your paper under "Preparation of UK Biobank data § Association analysis", you mention collapsing ultra-rare variants a la SAIGE-GENE+ and regenie:

Following Liu and Xie[25] and Zhou et al.,[27] we collapsed ultra-rare variants (those with a sample MAC ≤ 10) into a single pseudo-marker separately for each gene × variant category.

However it doesn't look like this is currently done automatically in this package. I think it would be very convenient if you encapsulated the logic to do so either into the main COAST functions (perhaps add a collapse_threshold_mac argument), or into a helper function that could be run to transform the genotype matrix and annotation vector beforehand.

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