small functionality patches to strand flip checks, dosage calculator, automated statistics #70
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| @@ -31,12 +31,16 @@ convert.alleles.to.pgs.dosage <- function(called.alleles, risk.alleles) { | |||
| } else { | |||
| # check that called.alleles is a vector of genotypes in allelic notation or '.' separated by a slash or pipe | |||
| # "*" characters represent overlapping deletions from an upstream indel and are accepted VCF format | |||
| allowed.pattern <- '^((([A-Z]+|\\.|\\*)[/\\|]([A-Z]+|\\.|\\*))|\\.)$' # '|' are special chars in regular expressions | |||
| allowed.pattern <- '^((([A-Z]+|\\.|\\*)[/\\|]([A-Z]+|\\.|\\*))|\\.|[A-Z]+)$' # '|' are special chars in regular expressions | |||
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You have some comments here about what individual characters mean. Is it possible to include an entire example? I think it would be helpful for interpretation.
forbiddenpersimmon
approved these changes
Feb 20, 2025
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Updates to strand flip checker functionality when handling INDELs: mark INDEL effect switches as "effect _switch"
Updates to dosage calculator to handle hemizygous genotypes: single alleles added to allowed allele format list, single alleles evaluated with haploid dosage (+ unit tests).
Updates to
apply.polygenic.scoreto more carefully filter data for statistical analyses.Update version to 3.0.1 (no breaking changes)
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].
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
NEWSunder the next release version or unreleased, and updated the date.I have updated the version number in
metadata.yamlandDESCRIPTION.Both
R CMD buildandR CMD checkrun successfully.Closes #...
Testing Results
All unit tests pass.