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add strand flip check #67

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add strand flip check #67

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This PR adds allele match checking and strand flip correction functionality.

Closes #63

  • Add DNA flip function (flips alleles to reverse complement)
  • Add allele match check function (checks for various mismatch cases including strand flip, and corrects strand flips)
  • Incorporate strand flip checking into the main apply.polygenic.score function
  • Add tests for above
  • Update all documentation (README, manual, vignette)
  • Export all relevant new functions through NAMESPACE
  • Update NEWS with new feature

This is a template for UCLA-CDS R package developers to create a github pull request template. Things should be adjusted for individual pipeline including:

  1. additional checklist items specific to the package
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  • The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)-[brief_description_of_branch].

  • I have set up or verified the branch protection rule following the github standards before opening this pull request.

  • I have added the changes included in this pull request to NEWS under the next release version or unreleased, and updated the date.

  • I have updated the version number in metadata.yaml and DESCRIPTION.

  • Both R CMD build and R CMD check run successfully.

Testing Results

All unit tests pass

@alkaZeltser alkaZeltser marked this pull request as draft October 31, 2024 01:01
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Add strand-flip handling
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