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.