MBR: Markov Blanket Resampling

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

Markov Blanket Resampling

Description

MBR This function performs the markov blanket resampling method according to Su and Borsuk, 2016.

Usage

MBR(
  source_net_adjacency,
  layers_def,
  omics,
  BGe_score_all_configs_node,
  parent_set_combinations
)

Arguments

source_net_adjacency	adajcency matrix of given network.
layers_def	data.frame containing the modality ID, corresponding layer in BN and maximal number of parents from given layer to GE nodes.
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.
parent_set_combinations	list of all possible parent set configuration for all nodes available.

Value

List of 10 elements needed to define adjacency matrix with markov blanket resampling

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)
adjacency_matrix <- OMICS_mod_res$B_prior_mat
adjacency_matrix[,] <- 0
MBR(source_net_adjacency = adjacency_matrix, 
    layers_def = OMICS_mod_res$layers_def, omics = OMICS_mod_res$omics, 
    BGe_score_all_configs_node = OMICS_mod_res$pf_UB_BGe_pre$BGe_score_all_configs_node,
    parent_set_combinations = OMICS_mod_res$pf_UB_BGe_pre$parents_set_combinations)

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