first_adapt_phase: 1st adaption phase

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

1st adaption phase

Description

first_adapt_phase 1st adaption phase of the adaptive MCMC: the variance of the proposal distribution is changed to achieve the MC acceptance rate of 0.44.

Usage

first_adapt_phase(
  omics,
  B_prior_mat,
  energy_all_configs_node,
  len,
  layers_def,
  prob_mbr,
  BGe_score_all_configs_node,
  parent_set_combinations,
  annot
)

Arguments

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.
energy_all_configs_node	list of nodes energy for all possible parent set configurations.
len	numeric vector initial width of the sampling interval for hyperparameter beta.
layers_def	data.frame containing the modality ID, corresponding layer in BN and maximal number of parents from given layer to GE nodes.
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 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(omics = OMICS_mod_res$omics, 
   B_prior_mat = OMICS_mod_res$B_prior_mat, len = 5, 
   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)

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