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daletovar opened this issue Jul 28, 2020 · 1 comment
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PBS API #73

daletovar opened this issue Jul 28, 2020 · 1 comment
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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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@daletovar
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I wanted to spark some discussion on what the api for doing pbs should look like. Based on this notebook that @alimanfoo made, it looks like we'll need to implement something like this:

  1. an allele count for each population.
    • sgkit.count_alleles will do this.
  2. locate and subset to segregating variants at sufficient frequency.
    • requires an is_biallelic_01 function, or something equivalent.
    • requires a to_frequencies function, or some equivalent operation.
  3. setup windows over the genome.
    • requires a moving_statistic function.
  4. calculate the PBS in a moving window.
    • requires a pbs function.
@ravwojdyla ravwojdyla added core operations Issues related to domain-specific functionality such as LD pruning, PCA, association testing, etc. enhancement New feature or request labels Jul 29, 2020
@jeromekelleher
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Closing in favour of #230.

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Labels
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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