transient_phase: transient phase

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

transient phase

Description

transient_phase This phase verify if the chain is moving towards the mode of target distribution.

Usage

transient_phase(
  first.adapt.phase_net,
  omics,
  B_prior_mat,
  layers_def,
  energy_all_configs_node,
  prob_mbr,
  BGe_score_all_configs_node,
  parent_set_combinations,
  annot
)

Arguments

first.adapt.phase_net	list output of the first.adapt.phase function.
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.
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.
prob_mbr	numeric vector probability of the MBR step.
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.
annot	named list containing the associated methylation probes of given gene.

Value

List of 1 element: first adaption phase and transient phase result

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)
first.adapt.phase_net <- first_adapt_phase(len = 5, 
    omics = OMICS_mod_res$omics, B_prior_mat = OMICS_mod_res$B_prior_mat, 
    energy_all_configs_node = 
    OMICS_mod_res$pf_UB_BGe_pre$energy_all_configs_node,
    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$parents_set_combinations, 
    annot = OMICS_mod_res$annot)
transient_phase(first.adapt.phase_net = first.adapt.phase_net, 
    omics = OMICS_mod_res$omics, B_prior_mat = OMICS_mod_res$B_prior_mat, 
    layers_def = OMICS_mod_res$layers_def, 
    energy_all_configs_node = 
    OMICS_mod_res$pf_UB_BGe_pre$energy_all_configs_node,
    prob_mbr = 0.07, annot = OMICS_mod_res$annot,
    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.