geno_strains.R

#' @title Create haplotype for a new mouse strain into a dataframe
#'
#' @description This functions adds columns for parental strains used in the cross in the annotation data frame, from the genotype data frame in which one or several animal of the parental strains were genotyped.
#' If several animals of one strain were genotyped, a consensus is created from these animals.
#' The consensus is created as follow : if the indivuals carry the same allele, this allele is kept, otherwise, the allele is noted as "N". If individuals show residual heterozygosity, it is encoded as "H".
#' @param ref data frame with the annotation of the arrray used
#' @param geno data frame with the genotyping results for your cross from miniMUGA array
#' @param par1 first parental strain used in the cross, the name must be written as in the geno data frame
#' @param par2 second parental strain used in the cross, the name must be written as in the geno data frame
#' @param name1 name of the first parental strain to use as the column name in the ref data frame
#' @param name2 name of the second parental strain to use as the column name in the ref data frame
#'
#' @import dplyr
#' @import tidyr
#'
#' @export
#'
geno_strains <- function(ref,geno,par1,par2,name1,name2){
  #rename df columns
  geno <- geno %>% rename("marker"=1,
                          "id"=2,
                          "allele_1"=3,
                          "allele_2"=4)


  #recode genotypes from 2 alleles to 1
  geno <- geno %>% mutate_all(as.character)
  geno <- geno %>% filter(id %in% c(par1,par2))
  geno <- geno %>% mutate(Geno=case_when(allele_1 == "-" | allele_2 == "-" ~ "N",
                                         allele_1 == allele_2 ~ allele_1,
                                         allele_1 %in% c("A","T","G","C") & allele_2 %in% c("A","T","G","C") ~ "H"))

  geno <- geno %>% select(marker,id,Geno) %>% pivot_wider(names_from = id, values_from = Geno)


  #create consensus
  geno <- geno %>% mutate(parent1 = !!sym(par1[1]))
  if(length(par1)!=1){
    for(i in 2:length(par1)){
      geno <- geno %>% mutate(parent1 = ifelse(parent1==!!sym(par1[i]),parent1,"N"))
    }
  }

  geno <- geno %>% mutate(parent2 = !!sym(par2[1]))
  if(length(par2)!=1){
    for(i in 2:length(par2)){
      geno <- geno %>% mutate(parent2 = ifelse(parent2==!!sym(par2[i]),parent2,"N"))
    }
  }

  geno <- geno %>% select(marker,parent1,parent2)
  colnames(geno) <- c("marker",name1,name2)

  #merge with ref file
  ref <- full_join(ref,geno,by=c("marker"="marker"))
  return(ref)
}