acceptance_check: Acceptance rate checking

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

Acceptance rate checking

Description

acceptance_check This phase verify if the acceptance is in range of 0.28 and 0.6.

Usage

acceptance_check(
  first.adapt.phase_net,
  round_check,
  last_iter_check,
  prob_mbr,
  layers_def,
  parent_set_combinations,
  BGe_score_all_configs_node,
  omics,
  annot
)

Arguments

first.adapt.phase_net	list output of the first.adapt.phase or source_net_def function.
round_check	numeric vector after each round_check iterations for which we calculate the beta acceptance rate.
last_iter_check	numeric vector number of the acceptance rate for the past last_iter_check iterations.
prob_mbr	numeric vector probability of the MBR step.
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.
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.
annot	named list containing the associated methylation probes of given gene.

Value

List of 1 element: first adaption phase result before given acceptance rate

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, TFtargs = TFtarg_mat,
    r_squared_thres = 0.3, lm_METH = TRUE)
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)
acceptance_check(first.adapt.phase_net = first.adapt.phase_net,
    round_check = 100, last_iter_check = 100, prob_mbr = 0.07,
    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$parents_set_combinations,
    omics = OMICS_mod_res$omics, annot = OMICS_mod_res$annot)

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