R/refineClusters.R

In maftools: Summarize, Analyze and Visualize MAF Files

dirichletClusters = function(tsb.dat){
  #Initiate mcmc parameters
  nburn = 1000
  nsave = 10000
  nskip = 20
  ndisplay = 1000
  mcmc = list(nburn=nburn,nsave=nsave,nskip=nskip,ndisplay=ndisplay)
  #Hyper parameters
  prior1 = list(alpha=0.05,m1=rep(0,1),psiinv1=diag(0.5,1),nu1=6,tau1=0.2,tau2=1000)
  #Run main function
  #dp = DPpackage::DPdensity(y = tsb.dat[,t_vaf]*100, prior = prior1, mcmc = mcmc, status = TRUE)
  #Assign clusters
  tsb.dat$cluster = as.character(dp$state$ss)
  return(tsb.dat)
}


refineClusters = function(clusters){
  totclusts = unique(clusters[,cluster])
  refinedClusters = c()

  for(i in 1:length(totclusts)){
    clust.dat = clusters[cluster == totclusts[i]]
    if(nrow(clust.dat) > 1){
      clust.dat = clusters[cluster == totclusts[i]]

      #Based on boxplot stats
      outl = boxplot.stats(x = clust.dat[,t_vaf])$out
      clust.dat$cluster = ifelse(test = clust.dat$t_vaf %in% outl, yes = 'outlier', no = clust.dat$cluster)

      #Based on zscore
      #clust.dat$z = scale(clust.dat[,t_vaf], center = TRUE, scale = TRUE)
      #clust.dat$cluster = ifelse(test = abs(clust.dat$z) >= 2.5 , no = clust.dat$cluster, yes = 'outlier')
      #clust.dat$cluster = ifelse(test = abs(clust.dat$z) >= 2.5 , no = clust.dat$cluster, yes = 'outlier')
      #clust.dat[,z := NULL]
    }else{
      clust.dat$cluster = 'outlier'
    }
    refinedClusters = rbind(refinedClusters, clust.dat)
  }

  temp.dat = refinedClusters[cluster %in% c('CN_altered', 'outlier')]
  refinedClusters = refinedClusters[!cluster %in% c('CN_altered', 'outlier')]

  clust.lvls = levels(factor(refinedClusters$cluster))
  refinedClusters$cluster = as.character(factor(refinedClusters$cluster, levels = clust.lvls, labels = 1:length(clust.lvls)))
  refinedClusters = rbind(refinedClusters, temp.dat)

  return(refinedClusters)
}