# Integrative analysis of multi-omics data to infer regulatory networks

## Documentation for package ‘IntOMICS’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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