clustDBN: DBN-based clustering
In bnClustOmics: Bayesian Network-Based Clustering of Multi-Omics Data

clustDBN

R Documentation

DBN-based clustering

Description

This function can be used for DBN-based clustering. It is the same function as bnclustOmics, but it also works for time series data.

Usage

clustDBN(
  dbndata,
  staticnodes = 0,
  blacklist = NULL,
  edgepmat = NULL,
  kclust = 2,
  chixi = 0.5,
  seed = 100,
  err = 1e-06,
  maxEM = 10,
  hardlim = 6,
  deltahl = 2,
  nit = 5,
  epmatrix = TRUE,
  plus1it = 4,
  nruns = 1,
  startpoint = "mclustPCA",
  baseprob = 0.4,
  commonspace = TRUE,
  verbose = TRUE,
  samestruct = TRUE,
  pickmax = TRUE
)

Arguments

`dbndata`	data matrix; rows are observations, columns are variables; static nodes have to be in the first column of the data
`staticnodes`	(integer) number of static nodes in a DBN
`blacklist`	adjacency matrix containing information about which edges will be blacklisted in structure search
`edgepmat`	penalization matrix of the edges in structure learning
`kclust`	the number of clusters (mixture components)
`chixi`	prior pseudocounts used for computing parameters for binary nodes
`seed`	integer number set for reproducibility
`err`	convergence criteria
`maxEM`	maximum number of EM iterations (structural)
`hardlim`	maximum number of parents per node when learning networks
`deltahl`	additional number of parents when sampling from the common search space
`nit`	number of internal iteration in structural EM
`epmatrix`	(logical) indicates if the matrices containing posterioir probabilities of single edges should be returned
`plus1it`	maximum number of search space expansion iterations when performing structure search
`nruns`	number of runs of the EM algorithm
`startpoint`	defines which algorithm is used to define starting cluster memberships: possible values "random", "mclustPCA" and "mclust"
`baseprob`	defines the base probability of cluster membership when "mclustPCA" or "mclust" used as starting point
`commonspace`	(logical) defines if the sampling has to be performed from the common search space
`verbose`	defines if the output messages should be printed
`samestruct`	(logical) defines if initial and intrinsic part of transition structures should be the same
`pickmax`	(logical) if TRUE only maximum EM run is returned