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.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.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.R CMD check CI/CD action with
renv dependency managementcreate.pgs.boxplotassess.pgs.vcf.allele.match to
condition the handling of ambiguous strand flips on the total number of
unambiguous strand flips.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.create.pgs.with.continuous.phenotype.plotapply.polygenic.score