acceptance_check | Acceptance rate checking |
annot | Genes and associated methylation probes |
beta_tuning | Beta tuning accessor |
bge_node | BGe score for specific node |
bge_score | BGe score |
bn_module | #' BN module |
BN_mod_res | IntOMICS MCMC simulation result |
borders_def | Color scales |
b_prior_mat | biological prior matrix |
B_prior_mat_weighted | Empirical biological knowledge accessor |
CPDAGs_sim1 | CPDAGs from the first simulation accessor |
CPDAGs_sim2 | CPDAGs from the second simulation accessor |
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_sapling_res | The MCMC_sapling_res class |
MCMC_sapling_res-class | The MCMC_sapling_res class |
mcmc_simulation_sampling_phase | Sampling phase |
neighborhood_size | Neighborhood size |
normalise | Arrow of directed edges tuning |
omics | Omics data |
OMICS_mod_res | preprocessed IntOMICS input 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 |
PK | Wnt signalling pathway |
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 |
TFtarg_mat | transcription factors and their known targets |
trace_plots | Trace plots of MCMC simulation |
transient_phase | transient phase |
variance_target | Second adaption phase variance tuning |
weighted_net | Resulting network definition |