Man pages for anna-pacinkova/intomics_package
Integrative analysis of multi-omics data to infer regulatory networks
| acceptance_check | Acceptance rate checking |
| annot | Genes and associated methylation probes |
| BGe_node | BGe score for specific node |
| BGe_score | BGe score |
| BN_mod_res | IntOMICS MCMC simulation result |
| BN_module | #' BN module |
| B_prior_mat | B_prior_mat |
| DAGcorescore | BGe score |
| edge_proposal | Markov Chain conventional single edge proposal move |
| edge_types | Resulting network definition |
| empB_heatmap | Heatmap of empB - B |
| energy_function_node_specific | Node energy function |
| epsilon | Epsilon |
| fan_in_reverse | Number of reverse edge candidates |
| first_adapt_phase | 1st adaption phase |
| gene_annot | Gene ID conversion table |
| init.net.mcmc | Random initial network |
| is.acyclic | Acyclic network identification. |
| layers_def | Gene ID conversion table |
| legend_custom | Node color |
| lm_meth | Linear regression GE~METH |
| MBR | Markov Blanket Resampling |
| MC3 | Markov Chain conventional single edge proposal move |
| MC3_constantBGe | Markov Chain conventional single edge proposal move with BGe... |
| mcmc.simulation_sampling.phase | Sampling phase |
| neighborhood_size | Neighborhood size |
| normalise | Arrow of directed edges tuning |
| omics | Omics data |
| OMICS_module | OMICS_module |
| parent_sets_sum_scores_childrenX | 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 |
| sample.chain | Random initial network edge generation |
| sampling_phase | Sampling phase |
| scoreparameters_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 & resulting network definition |
| transient_phase | transient phase |
| variance_target | Second adaption phase variance tuning |
