second_adapt_phase: Second adaption phase

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

Second adaption phase

Description

second_adapt_phase This phase identifies the proposal distribution that has a similar covariance structure with the target distribution.

Usage

second_adapt_phase(
  transient.phase_net,
  omics,
  layers_def,
  B_prior_mat,
  energy_all_configs_node,
  prob_mbr,
  BGe_score_all_configs_node,
  parent_set_combinations,
  annot,
  woPKGE_belief = 0.5
)

Arguments

transient.phase_net	list output of the transient.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.
layers_def	data.frame containing the modality ID, corresponding layer in BN and maximal number of parents from given layer to GE nodes.
B_prior_mat	a biological prior matrix.
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.
woPKGE_belief	numeric vector to define the belief concerning GE-GE interactions without prior knowledge (default=0.5).

Value

List of 1 element: first adaption phase + transient phase + second adaption phase result

Examples

data(list=c("PK", "TFtarg_mat", "annot", "layers_def", "omics"),
     package="IntOMICS")
OMICS_mod_res <- OMICS_module(omics = omics, PK = PK, annot = annot, 
     layers_def = layers_def, lm_METH = TRUE,
     TFtargs = TFtarg_mat, 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, 
    energy_all_configs_node = 
    OMICS_mod_res$pf_UB_BGe_pre$energy_all_configs_node,
    len = 5, prob_mbr = 0.07, annot = OMICS_mod_res$annot,
    layers_def = OMICS_mod_res$layers_def, 
    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)
transient.phase_net <- transient_phase(prob_mbr = 0.07,
    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$layers_def, annot = OMICS_mod_res$annot,
    energy_all_configs_node = 
    OMICS_mod_res$pf_UB_BGe_pre$energy_all_configs_node,
    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) 
second_adapt_phase(transient.phase_net = transient.phase_net,
    omics = OMICS_mod_res$omics, B_prior_mat = OMICS_mod_res$B_prior_mat, 
    layers_def = OMICS_mod_res$layers_def, woPKGE_belief = 0.5,
    energy_all_configs_node = 
    OMICS_mod_res$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.