012或0-11格式转换

#' convert an intact (without missing values) genotyped matrix, sample x genotype, 
#' into 012 coding format, used for add, dom, or epi analysis
#'
#' @param genotype 
#'
#' @return
#' @export
#'
#' @examples
genoTo012 <- function(genotype) {
  allel_all <- genotype %>% str_split("") %>% unlist
  allel_uni=unique(allel_all)
  allel_tab=table(allel_all)
  allel_min=names(allel_tab[which.min(allel_tab)])
  allel_max=allel_uni[allel_uni!=allel_min]
  geno_2=paste0(allel_min,allel_min)
  geno_0=paste0(allel_max,allel_max)
  genotype[which(genotype==geno_0)]=0
  genotype[which(genotype==geno_2)]=2
  genotype[which(genotype!=0&genotype!=2)]=1
  genotype=as.numeric(genotype)
  return(genotype)
}
#' convert an intact (without missing values) genotyped matrix, sample x genotype, 
#' into 0,-1,1 coding format, used for imprinting analysis
#'
#' @param genotype 
#'
#' @return
#' @export
#'
#' @examples
genoTo01_12 <- function(genotype) {
  allel_all <- genotype %>% str_split("") %>% unlist
  allel_uni=unique(allel_all)
  allel_tab=table(allel_all)
  allel_min=names(allel_tab[which.min(allel_tab)])
  allel_max=allel_uni[allel_uni!=allel_min]
  
  geno_1=paste0(allel_min,allel_max)
  geno__1=paste0(allel_max,allel_min)
  genotype[which(genotype==geno_1)]=1
  genotype[which(genotype==geno__1)]=-1
  genotype[which(genotype!=1&genotype!=-1)]=0
  genotype=as.numeric(genotype)
  return(genotype)
}