#' HBD/FLOD recap
#'
#' This function creates HBD and FLOD recap dataframe.
#'
#' @param atlas a atlas object
#' @param recap.by.segments : whether you want the recap by segments or snps
#'
#' @details For each individual and each marker the function computes
#' @details the mean value of every HBD probabilities computed through the submaps.
#' @details The same is done with the FLOD scores.
#' @details This function returns a list of two dataframes with HBD and FLOD in it.
#'
#' @seealso Fantasio
#' @seealso makeAtlasByDistance
#' @seealso segmentsListByHotspots
#' @seealso festim
#' @seealso setHBDProb
#' @seealso setFLOD
#' @seealso setHFLOD
#' @seealso HBDSegments
#'
#' @return This function returns a list of dataframes.
#'
#' @export
recap <- function(atlas, recap.by.segments = atlas@bySegments) {
if(class(atlas@submaps_list[[1]])[1] != "snpsMatrix" & class(atlas@submaps_list[[1]])[1] != "HostspotsMatrix")
stop("need either an hotspots.segments list of submaps or a snpsSegments list of submaps.")
if(class(atlas@bedmatrix)[1] != "bed.matrix")
stop("Need a bed.matrix.")
if(length(atlas@submaps_list) == 1) {
matrice_HBD <- atlas@submaps_list[[1]]@HBD.prob
matrice_FLOD <- atlas@submaps_list[[1]]@FLOD
l <- list(matrice_HBD, matrice_FLOD)
return(l)
}
# HBD probabilities and FLOD scores
proba_HBD <- submapHBDRecap(atlas)
FLOD <- submapFLODRecap(atlas)
if(recap.by.segments) {
recapBySegments(atlas, proba_HBD, FLOD)
} else {
recapBySnps(atlas, proba_HBD, FLOD)
}
}
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