fix code chunk in manual typo

R/apply-pgs.R

@@ -146,7 +146,7 @@ validate.phenotype.data.input <- function(phenotype.data, phenotype.analysis.col
 #' The PGS catalog standard column \code{other_allele} in \code{pgs.weight.data} is required for this check.
 #' @param remove.ambiguous.allele.matches A logical indicating whether to remove PGS variants with ambiguous allele matches between PGS weight data and VCF genotype data. Default is \code{FALSE}.
 #' The PGS catalog standard column \code{other_allele} in \code{pgs.weight.data} is required for this check.
-#' @param max.strand.flips An integer indicating the number of unambiguous strand flips that need to be detected in order to discard all variants with ambiguous allele matches. Only applies if {return.ambiguous.as.missing == TRUE}.
+#' @param max.strand.flips An integer indicating the number of unambiguous strand flips that need to be detected in order to discard all variants with ambiguous allele matches. Only applies if \code{return.ambiguous.as.missing == TRUE}.
 #' Default is \code{0} which means that all ambiguous variants are removed regardless of the status of any other variant.
 #' @param remove.mismatched.indels A logical indicating whether to remove indel variants that are mismatched between PGS weight data and VCF genotype data. Default is \code{FALSE}.
 #' The PGS catalog standard column \code{other_allele} in \code{pgs.weight.data} is required for this check.

R/assess-strand-flip.R

@@ -93,7 +93,7 @@ flip.DNA.allele <- function(alleles, return.indels.as.missing = FALSE) {
 #' @param return.indels.as.missing A logical value indicating whether to return NA for INDEL alleles with detected mismatches. Default is \code{FALSE}.
 #' @param return.ambiguous.as.missing A logical value indicating whether to return NA for ambiguous cases where both a strand flip and effect switch are possible,
 #' or no strand flip is detected and a mismatch cannot be resolved. Default is \code{FALSE}.
-#' @param max.strand.flips An integer indicating the number of non-ambiguous strand flips that must be present to implement the discarding all allele matches labeled "ambiguous_flip". Only applies if {return.ambiguous.as.missing == TRUE}.
+#' @param max.strand.flips An integer indicating the number of non-ambiguous strand flips that must be present to implement the discarding all allele matches labeled "ambiguous_flip". Only applies if \code{return.ambiguous.as.missing == TRUE}.
 #' Defaults to \code{0}, meaning that no strand flips are allowed. Allele matches labeled "unresolved_mismatch" are not affected by this parameter.
 #' @return A list containing the match assessment, a new PGS effect allele, and a new PGS other allele.
 #'