R/get.mcl.clustering.R

In chulingding/MultiSEPhyR: Multi-Sample EPIC Phylogenetic Reconstruction

#' get.mcl.clustering
#'
#' `get.mcl.clustering` uses the MCL clustering algorithm to define copy number events.
#'
#'
#' @return Returns the clustering results and the length of each paticular segment.
#' @importFrom magrittr %>%
#'
#' @export

get.mcl.clstering <- function(df, max.iter = 500){
  M_dist <- 0.9 - mahalanobis.dist(df[,-c(1:3)])
  M_dist[M_dist < 0] <- 0
  res.mcl <- mcl(M_dist, addLoops = T, max.iter = max.iter)

  cluster <- cbind(df,as.character(res.mcl$Cluster))
  colnames(cluster)[7] <- "cluster"
  cluster[,"length"] <- cluster$end - cluster$start
  return(cluster)
}