Integrative analysis of multi-omics data to infer regulatory networks


[Up] [Top]

Documentation for package ‘IntOMICS’ version 1.2.0

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