NEWS

ApplyPolygenicScore 4.0.2 (2026-02-26)

Updated import.vcf INFO-field tests to be robust to upstream vcfR::vcfR2tidy() schema additions (e.g., VariantKey) and avoid CRAN failures.

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 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.

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 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.

Added hemizygous allele handling to dosage calculation
Added toggle to hexbinplot at sample size threshold in create.pgs.with.continuous.phenotype.plot

Updated INDEL effect switch reporting by strand flip checker
Updated data structuring for automated statistical analysis in apply.polygenic.score

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

Renamed functions starting with reserved vocabulary for S3 generic methods merge. -> combine.