Unreleased

ApplyPolygenicScore 4.0.2

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

Changed

• Updated Paul Boutros email to @sbpdiscovery.org

ApplyPolygenicScore 4.0.0

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

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 (2024-12-02)

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 (2024-07-31)

Changed

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

ApplyPolygenicScore 1.0.0 (2024-07-25)

• First release

ApplyPolygenicScore 0.1.0 (2024-07-25)

• INITIAL FEATURES