source_net_def: Source network for MCMC simulation

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

Source network for MCMC simulation

Description

source_net_def This function is used to create the initial network with its features necessary for MCMC simulation.

Usage

source_net_def(
  init.net.mcmc.output,
  parent_set_combinations,
  omics,
  BGe_score_all_configs_node,
  B_prior_mat,
  layers_def,
  energy_all_configs_node,
  len
)

Arguments

init.net.mcmc.output	list output of the init.net.mcmc function.
parent_set_combinations	list of all possible parent set configuration for all nodes available.
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.
BGe_score_all_configs_node	list of nodes BGe score for all possible parent set configurations.
B_prior_mat	a biological prior matrix.
layers_def	data.frame containing the modality ID, corresponding layer in BN and maximal number of parents from given layer to GE nodes.
energy_all_configs_node	list of nodes energy for all possible parent set configurations.
len	numeric vector initial width of the sampling interval for hyperparameter beta.

Value

List of 10 elements needed to define the initial adjacency matrix

Examples

data(list=c("PK", "TFtarg_mat", "annot", "layers_def", "omics"),
package="IntOMICS")
OMICS_mod_res <- OMICS_module(omics = omics, PK = PK, 
    layers_def = layers_def, TFtargs = TFtarg_mat, annot = annot, 
    r_squared_thres = 0.3, lm_METH = TRUE)
init.net <- init.net.mcmc(omics = OMICS_mod_res$omics, 
    layers_def = OMICS_mod_res$layers_def, 
    B_prior_mat = OMICS_mod_res$B_prior_mat)
source_net_def(init.net.mcmc.output = init.net, 
    omics = OMICS_mod_res$omics, 
    parent_set_combinations = OMICS_mod_res$pf_UB_BGe_pre$parents_set_combinations,
    BGe_score_all_configs_node = OMICS_mod_res$pf_UB_BGe_pre$BGe_score_all_configs_node, 
    B_prior_mat = OMICS_mod_res$B_prior_mat, 
    layers_def = OMICS_mod_res$layers_def, len = 5,
    energy_all_configs_node = OMICS_mod_res$pf_UB_BGe_pre$energy_all_configs_node)
             

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