BGe_score: BGe score

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

BGe score

Description

BGe_score Computes the BGe score of given network using precomputed sets of possible parents.

Usage

BGe_score(
  adjacency_matrix,
  omics,
  layers_def,
  parent_set_combinations,
  BGe_score_all_configs_node
)

Arguments

adjacency_matrix	adjacency matrix of given network.
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.
layers_def	data.frame containing the modality ID, corresponding layer in BN and maximal number of parents from given layer to GE nodes.
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.

Value

Numeric vector of length 1: BGe score of given adjacency matrix

Examples

data(list=c("PK", "TFtarg_mat", "annot", "layers_def", "omics"),
    package="IntOMICS")
OMICS_mod_res <- OMICS_module(omics = omics, PK = PK, lm_METH = TRUE,
    layers_def = layers_def, TFtargs = TFtarg_mat, annot = annot, 
    r_squared_thres = 0.3)
first.adapt.phase_net <- first_adapt_phase(omics = OMICS_mod_res$omics, 
    B_prior_mat = OMICS_mod_res$B_prior_mat, annot = OMICS_mod_res$annot,
    energy_all_configs_node = OMICS_mod_res$pf_UB_BGe_pre$energy_all_configs_node,
    len = 5, layers_def = OMICS_mod_res$layers_def, prob_mbr = 0.07,
    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)
adjacency_matrix <- OMICS_mod_res$B_prior_mat
adjacency_matrix[,] <- 0
BGe_score(adjacency_matrix = adjacency_matrix, omics = OMICS_mod_res$omics,
    layers_def = OMICS_mod_res$layers_def, 
    parent_set_combinations =
    OMICS_mod_res$pf_UB_BGe_pre$parents_set_combinations, 
    BGe_score_all_configs_node = OMICS_mod_res$pf_UB_BGe_pre$BGe_score_all_configs_node)

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