mcmc.simulation_sampling.phase: Sampling phase

In anna-pacinkova/intomics_package: Integrative analysis of multi-omics data to infer regulatory networks

Sampling phase

Description

mcmc.simulation_sampling.phase This function performs the final sampling of network structures with estimated hyperparameters. It if part of sampling_phase function.

Usage

mcmc.simulation_sampling.phase(
  first,
  last,
  sim_init,
  prob_mbr,
  B_prior_mat,
  omics,
  parent_set_combinations,
  BGe_score_all_configs_node,
  layers_def,
  len,
  thin,
  energy_all_configs_node,
  annot
)

Arguments

first	numeric vector iteration to start.
last	numeric vector iteration to stop.
sim_init	list output from the source_net_def function or from two independent simulations from the mcmc.simulation_sampling.phase function.
prob_mbr	numeric vector probability of the MBR step.
B_prior_mat	a biological prior matrix.
omics	named list containing the gene expression (possibly copy number variation and methylation data). Each component of the list is a matrix with samples in rows and features in columns.
parent_set_combinations	list of all possible parent set configuration for all nodes available.
BGe_score_all_configs_node	list of nodes BGe score for all possible parent set configurations.
layers_def	data.frame containing the modality ID, corresponding layer in BN and maximal number of parents from given layer to GE nodes.
len	numeric vector initial width of the sampling interval for hyperparameter beta.
thin	numeric vector thinning frequency of the resulting MCMC simulation.
energy_all_configs_node	list of nodes energy for all possible parent set configurations.
annot	named list containing the associated methylation probes of given gene. importFrom bnlearn empty.graph amat cpdag importFrom stats runif

Value

List of 1 element: sampling phase result before MCMC convergence

anna-pacinkova/intomics_package documentation built on Aug. 13, 2022, 11:38 a.m.