R/majorminor.R

In rystanley/genepopedit: Simple and flexible manipulation of genomic data

# BGC Allele conversion - this function is built specifically for genepop_bgc in genepopedit
#' @title Function to convert allele in character format to bgc zygosity format.
#' @description sub-function used by genepop_bgc
#' @param Vec Vector of characters representing alleles.
#' @param allele_length The number of characters in an allele (default: 6 e.g. 130120).
#' @rdname majorminor
#' @export

majorminor<- function(Vec, allele_length = 6){
  if(sum(is.na(Vec))!=length(Vec)){
  Vec <- as.character(Vec)
  firstAllele <-  as.data.frame(sapply(Vec,function(x)as.character(substring(x,1,(allele_length/2)))),stringsAsFactors = F)
  secondAllele <-  as.data.frame(sapply(Vec,function(x)as.character(substring(x,(allele_length/2)+1,allele_length))),stringsAsFactors = F)
  x=c(firstAllele[,1],secondAllele[,1])
  AlleleMajor <- as.character(names(which(table(x)==max(table(x)))))
  AlleleMinor <- as.character(names(which(table(x)==min(table(x)))))
  if(length(AlleleMajor)>1){AlleleMajor <- AlleleMajor[1];AlleleMinor=AlleleMinor[2]}

  Vec[is.na(Vec)]="-9 -9" #missing data
  Vec=gsub(paste0(AlleleMajor,AlleleMajor),"2 0",Vec) #homozygous major
  Vec=gsub(paste0(AlleleMajor,AlleleMinor),"1 1",Vec) #heterozygous
  Vec=gsub(paste0(AlleleMinor,AlleleMajor),"1 1",Vec) #heterozygous
  Vec=gsub(paste0(AlleleMinor,AlleleMinor),"0 2",Vec) #homozygous minor
  } else {Vec=rep("0 0",length(Vec))}
  return(Vec)
}