R/as.data.frame.pedigree.R

In sinnweja/kinship2: Pedigree Functions

#' data.frame from a pedigree object
#'
#' @description
#' Extract the internal data from a pedigree object into a data.frame
#'
#' @param x Pedigree object
#' @param ... Additional arguments passed to internal methods
#'
#' @return A data.frame with the data necessary to re-create the pedigree,
#' minus special relationships.
#'
#' @examples
#' data(sample.ped)
#' ped <- with(sample.ped, pedigree(id, father, mother, sex, affected))
#' as.data.frame.pedigree(ped)
#'
#' @author Jason Sinnwell
#' @seealso \code{\link{pedigree}}
#' @export as.data.frame.pedigree
as.data.frame.pedigree <- function(x, ...) {
  dadid <- momid <- rep(0, length(x$id))
  dadid[x$findex > 0] <- x$id[x$findex]
  momid[x$mindex > 0] <- x$id[x$mindex]
  df <- data.frame(id = x$id, dadid = dadid, momid = momid, sex = x$sex)

  if (!is.null(x$affected)) {
    df$affected <- x$affected
  }

  if (!is.null(x$status)) {
    df$status <- x$status
  }
  return(df)
}