add strand flip smart check

[alkaZeltser]

In this PR:

• new option in assess.pgs.vcf.allele.match that conditions ambiguous strand flip removal on the number of detected unambiguous allele matches.
• extended above option to main pgs function
• updated docs with new info including vignettes
• added unit tests for above

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• 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].

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• 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]

Hey @jarbet I don't think I have access to request Copilot for a review. Could you give it a go again?

[Copilot]

Pull Request Overview

This PR introduces a new max.strand.flips option to condition ambiguous strand flip handling on the count of unambiguous flips, extends it through apply.polygenic.score, updates documentation and vignettes, and adds corresponding unit tests.

• Add max.strand.flips argument to assess.pgs.vcf.allele.match and apply.polygenic.score
• Update vignette and man pages to document new behavior
• Introduce unit tests covering threshold logic in both allele matching and PGS application

Reviewed Changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
vignettes/UserGuide.Rmd	Added max.strand.flips and custom pgs.columns notes; updated plotting list
tests/testthat/test-strand-flip-handling.R	New tests for ambiguous flip threshold behavior
tests/testthat/test-pgs-application.R	New end-to-end tests for max.strand.flips in PGS application
man/assess.pgs.vcf.allele.match.Rd	Documented max.strand.flips parameter
man/apply.polygenic.score.Rd	Documented max.strand.flips parameter
R/assess-strand-flip.R	Implemented threshold logic and roxygen updates
R/apply-pgs.R	Pass and adjust max.strand.flips through main flow
NEWS.md	Added release note for conditional strand flip removal

Comments suppressed due to low confidence (2)

man/apply.polygenic.score.Rd:43

• Update the documentation to reference the correct high-level argument name (remove.ambiguous.allele.matches) and wrap the condition in \code{} instead of braces.

\item{max.strand.flips}{An integer indicating the number of unambiguous strand flips that need to be detected in order to discard all variants with ambiguous allele matches. Only applies if {return.ambiguous.as.missing == TRUE}.

R/assess-strand-flip.R:82

• Wrap parameter references in \code{} (e.g., \code{return.ambiguous.as.missing == TRUE}) and correct the spelling of "ambigous_flip" to "ambiguous_flip" in the roxygen comment.

#' @param max.strand.flips An integer indicating the number of non-ambiguous strand flips that must be present to implement the discarding all allele matches labeled "ambigous_flip". Only applies if {return.ambiguous.as.missing == TRUE}.