#'Find HBDsegments
#'
#'This function creates HBDsegments used for creating plots
#'
#' @param submaps a atlas object
#' @param n.consecutive.markers the number of consecutive markers with a probabilitie equal or greater to the value of the threshold, to be use to fing HBDsegments (default is 5)
#' @param threshold the minimum value of HBD probabilities given for a marker (default is 0.5)
#'
#' @details The threshold is the minimum value from which we consider the marker is HBD. From this marker we want a minumum number of consecutive markers to create a HBD segment.
#' (argument : n.consecutive.markers)
#'
#' @return This function returns a list of dataframe with 11 columns :
#' @return - id
#' @return - famid
#' @return - pheno
#' @return - start
#' @return - end
#' @return - size
#' @return - chromosome
#' @return - start_pos
#' @return - end_pos
#' @return - start_dist
#' @return - end_dist
#'
#' @seealso setSummary
#' @seealso setHBDProb
#'
#' @keywords internal
HBDSegments <- function(submaps, n.consecutive.markers = 5, threshold = 0.5)
{
if(submaps@bySegments)
{
HBDSegmentsBySegments(submaps, submaps@HBD_recap, n.consecutive.markers, threshold)
}
else
{
HBDSegmentsBySnps(submaps, submaps@HBD_recap, n.consecutive.markers, threshold)
}
}
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