tests/testthat/helper-test-utils.R

In ApplyPolygenicScore: Utilities for the Application of a Polygenic Score to a VCF

initialize.defaults <- function() {
    phenotype.data <- NULL
    phenotype.analysis.columns <- NULL
    correct.strand.flips <- TRUE
    remove.ambiguous.allele.matches <- FALSE
    max.strand.flips <- 0
    remove.mismatched.indels <- FALSE
    output.dir <- NULL
    file.prefix <- NULL
    missing.genotype.method <- 'mean.dosage'
    use.external.effect.allele.frequency <- FALSE
    n.percentiles <- NULL
    analysis.source.pgs <- NULL
    validate.inputs.only <- FALSE
    }