BN_mod_res              IntOMICS MCMC simulation result
B_prior_mat_weighted    Empirical biological knowledge accessor
CPDAGs_sim1             CPDAGs from the first simulation accessor
CPDAGs_sim2             CPDAGs from the second simulation accessor
MCMC_sapling_res        The MCMC_sapling_res class
OMICS_mod_res           preprocessed IntOMICS input data
PK                      Wnt signalling pathway
TFtarg_mat              transcription factors and their known targets
acceptance_check        Acceptance rate checking
annot                   Genes and associated methylation probes
b_prior_mat             biological prior matrix
beta_tuning             Beta tuning accessor
bge_node                BGe score for specific node
bge_score               BGe score
bn_module               #' BN module
borders_def             Color scales
dag_core_score          BGe score
dens_edge_weights       Density plot of edge weights inferred by
                        IntOMICS
edge_proposal           Markov Chain conventional single edge proposal
                        move
edge_types              Resulting edge types definition
edge_weights            Edge weights of MCMC simulation
emp_b_heatmap           Heatmap of empB - B
energy_function_node_specific
                        Node energy function
epsilon                 Epsilon
estimated_beta          Estimated beta accessor
estimated_len           Estimated len accessor
fan_in_reverse          Number of reverse edge candidates
first.adapt.phase_net   IntOMICS first adaption phase result
first_adapt_phase       1st adaption phase
gene_annot              Gene ID conversion table
ggraph_weighted_net     Regulatory network plot with edge labels
init_net_mcmc           Random initial network
is_acyclic              Acyclic network identification.
layers_def              Layers definition of all omics data
legend_custom_ggplot    Node color legend
lm_meth                 Linear regression GE~METH
mbr                     Markov Blanket Resampling
mc3                     Markov Chain conventional single edge proposal
                        move
mc3_constant_bge        Markov Chain conventional single edge proposal
                        move with BGe score fixed
mcmc_simulation_sampling_phase
                        Sampling phase
neighborhood_size       Neighborhood size
normalise               Arrow of directed edges tuning
omics                   Omics data
omics_to_list           Convert omics MultiAssayExperiment to list
parent_sets_sum_scores_children_x
                        MBR sum of children scores
parent_sets_sum_scores_x
                        MBR sum of scores
pf_ub_est               Partition function upper bound
range_01                Range between 0 and 1
rms                     c_rms trace accessor
sample_chain            Random initial network edge generation
sampling_phase          Sampling phase
score_parameters_bidag_bge
                        BGe score parameters
second_adapt_phase      Second adaption phase
source_net_def          Source network for MCMC simulation
squared_jumping         Squared jumping of adaptive MCMC algorithm
trace_plots             Trace plots of MCMC simulation
transient_phase         transient phase
variance_target         Second adaption phase variance tuning
weighted_net            Resulting network definition
