Integrative analysis of multi-omics data to infer regulatory networks

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Documentation for package ‘IntOMICS’ version 1.0.0

• 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