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Improvements to PCA steps & default reference panel #133

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smlmbrt opened this issue Jul 31, 2023 · 1 comment
Open
1 of 3 tasks

Improvements to PCA steps & default reference panel #133

smlmbrt opened this issue Jul 31, 2023 · 1 comment
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@smlmbrt @joeltg10
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enhancement New feature or request

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smlmbrt commented Jul 31, 2023 •
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Ideas for making PCA projections more robust

  • Subsetting to a smaller set of PCA eligible variants?
    • HapMap3 (same as bigsnpr)
    • Ancestry informative markers (similar to Hao et al.), such as those in doi:10.3389/fgene.2012.00322
  • Avoid variants with high missingness in target dataset (use .vmiss files)
    • Implemented in beta release
  • Add back OCE samples to reference panel, but exclude from empirical calculation of Z-scores due to low number of individuals for comparison.
@smlmbrt smlmbrt added the enhancement New feature or request label Jul 31, 2023
@smlmbrt smlmbrt added this to the v2.1.0 milestone Jul 31, 2023
@smlmbrt smlmbrt changed the title Additional reference panels Improved population reference panels Aug 3, 2023
@smlmbrt smlmbrt changed the title Improved population reference panels Potential improvements to PCA Feb 26, 2024
@smlmbrt smlmbrt changed the title Potential improvements to PCA Potential improvements to PCA steps Feb 26, 2024
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smlmbrt commented Feb 26, 2024

Previously implemented:

@smlmbrt smlmbrt linked a pull request Mar 25, 2024 that will close this issue
Improve pca #267
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@smlmbrt smlmbrt self-assigned this Mar 26, 2024
@smlmbrt smlmbrt changed the title Potential improvements to PCA steps Improvements to PCA steps & default reference panel Jun 19, 2024
@smlmbrt smlmbrt removed this from the v2.0.0-beta.1 milestone Jun 19, 2024
@smlmbrt smlmbrt removed a link to a pull request Aug 2, 2024
Improve pca #267
Merged
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