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Update popgen stats to compute for all variants #238

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jeromekelleher opened this issue Sep 8, 2020 · 1 comment
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Update popgen stats to compute for all variants #238

jeromekelleher opened this issue Sep 8, 2020 · 1 comment
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core operations Issues related to domain-specific functionality such as LD pruning, PCA, association testing, etc.

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@jeromekelleher
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#100 added support for some basic popgen stats. However, these all currently return a single value, which contradicts the idiom that we are establishing of "every function returns an updated dataset" (#103). I think the default behaviour of these functions should be to return the full array of values in the updated dataset, for example, in the diversity function we'd add a new variable stats_diversity which is assigned the value of pi that we have computed (before summing).

This would include the Fst (#225) statistic, so is part of #232 and #226.

@jeromekelleher jeromekelleher added the core operations Issues related to domain-specific functionality such as LD pruning, PCA, association testing, etc. label Sep 8, 2020
@tomwhite
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tomwhite commented Nov 5, 2020

This was fixed in #303 and documented in #361

@tomwhite tomwhite closed this as completed Nov 5, 2020
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