#' @title Exclude markers depending on proportions of homo/hetorozygous
#'
#' @description uses the dataframe produced by the tab_mark function and fills the "exclude" column for all the markers that present odd proportions of each genotype. You can define these proportions thanks to the arguments of the function.
#' @param tab data frame obtained with tab_mark function.
#' @param cross F2 or N2.
#' @param homo proportion of homozygous individuals under which the marker is excluded. Will apply on both homozygous genotypes for a F2, but only on one for N2.
#' @param hetero proportion of heterozygous individuals under which the marker is excluded.
#' @param na proportion of non-genotyped individuals above which the marker is excluded.
#'
#' @import dplyr
#'
#' @export
#'
#### mark_prop ####
## excludes markers depending on proportions of homo/hetorozygous
#' @title Create of the summary table for all markers from the genotype data frame
#'
#' @description This function creates a table with all the markers that were genotyped in the array, the alleles for these markers, the number of homozygous and heterozygous animals, as well as the number of non genotyped animals.
#' @param geno data frame with the genotyping results for your cross
#' @title Exclude markers that were not genotyped in the reference strains
#'
#' @description This functions uses the dataframe produced by the tab_mark function and fills the "exclude" column for all the markers that were genotyped in the individuals of the cross but not in the reference strains. This is useful if the parental strains of the cross were not genotyped with the individuals and a previous genotyping result is used. Indeed, changes in the markers of the array may have happened. We recommend always using this function in order to avoid errors.
#' @param tab data frame obtained with tab_mark function
#' @param ref data frame with the reference genotypes of mouse lines
#'
#' @import dplyr
#'
#' @export
#'
mark_match <- function(tab, #tab_mark df
ref){ #strain ref geno file
#finds SNPs that are in both files:
snp_strains <- as.character(ref$marker) #extracts SNPs in strains ref geno file
snp_genfile <- as.character(tab$marker) #extracts SNPs in cross geno file
snp <- intersect(snp_strains,snp_genfile) #take intercept
#' @title Create of the summary table for all markers from the genotype data frame
#'
#' @description This function creates a table with all the markers that were genotyped in the array, the alleles for these markers, the number of homozygous and heterozygous animals, as well as the number of non genotyped animals.
#' @param geno data frame with the genotyping results for your cross
