NEWS
ApplyPolygenicScore 4.0.2 (2026-02-26)
Changed
- Updated
import.vcf INFO-field tests to be robust to upstream vcfR::vcfR2tidy() schema additions (e.g., VariantKey) and avoid CRAN failures.
ApplyPolygenicScore 4.0.1 (2026-01-23)
Changed
ApplyPolygenicScore 4.0.0 (2025-08-20)
Changed
- Refactored all main functions for gains in RAM efficiency and runtime
- Introduced a breaking change to the output of
import.vcf. The outputed list object has a different naming scheme and different data formats. Previous data formats are still supported by setting long.format to TRUE, however the naming scheme is still changed.
- Introduced a breaking change to
apply.polygenic.score. The expected default vcf.data input format has changed. The previous input format is still supported by setting vcf.long.format to TRUE from the default FALSE.
Added
- Added support for more efficient storage and manipulation of imported VCF data. The default output of
import.vcf now returns VCF data in a split format. A data.table object contains VCF data from fixed fields (CHROM, POS, ID, REF, ALT). A matrix object contains sample-specific genotypes in allele-format in a sample (columns) by variant (rows) matrix.
ApplyPolygenicScore 3.1.0
Changed
- Fixed regression of combine.vcf.with.pgs() function that prevented it from handling multiple rsIDs on the same line.
- Fixed bug caused by the case of a sample-specific missing variant at a multiallelic site
- Use updated
R CMD check CI/CD action with renv dependency management
Added
- Added new contributor
- Added minimum sample size check for grouped density curves
- Added new plotting function
create.pgs.boxplot
- Added option for user to provide custom PGS source column(s) for plotting functions
- Added option to
assess.pgs.vcf.allele.match to condition the handling of ambiguous strand flips on the total number of unambiguous strand flips.
- Added new function
analyze.pgs.binary.predictiveness which given a PGS and phenotypes runs a logistic regression and returns statistics (OR, p-value, AUC) describing how well the PGS predicts the phenotype. It also automatically plots a receiver-operator-curve.
ApplyPolygenicScore 3.0.2
Changed
- ApplyPolygenicScore released on CRAN! Updated README with CRAN links.
ApplyPolygenicScore 3.0.1 (2025-03-05)
Added
- Added hemizygous allele handling to dosage calculation
- Added toggle to hexbinplot at sample size threshold in
create.pgs.with.continuous.phenotype.plot
Changed
- Updated INDEL effect switch reporting by strand flip checker
- Updated data structuring for automated statistical analysis in
apply.polygenic.score
ApplyPolygenicScore 3.0.0
Added
- Added handling of overlapping deletion allele notation
- Added secondary PGS/VCF variant matching method using rsID after first attempt with genomic coordinates
- Added checks for rsID as an optional column in input PGS weight files
- Added functionality to assess allele matches and correct strand flips
ApplyPolygenicScore 2.0.0
Changed
- Renamed functions starting with reserved vocabulary for S3 generic methods merge. -> combine.
ApplyPolygenicScore 1.0.0
ApplyPolygenicScore 0.1.0