OMICS_module: OMICS_module

In anna-pacinkova/intomics_package: Integrative analysis of multi-omics data to infer regulatory networks

OMICS_module

Description

OMICS_module data preprocessing + B_prior_mat definition + partition function upper bound estimation + all possible parent sets per node definition + BGe score computation for all possible parent sets

Usage

OMICS_module(
  omics,
  PK = NULL,
  layers_def,
  TFtargs = NULL,
  annot = NULL,
  lm_METH = TRUE,
  r_squared_thres = 0.3,
  p_val_thres = 0.05,
  TFBS_belief = 0.75,
  nonGE_belief = 0.5,
  woPKGE_belief = 0.5
)

Arguments

omics	named list containing the gene expression (possibly copy number variation and methylation data). Each component of the list is a matrix with samples in rows and features in columns.
PK	data.frame with known interactions.
layers_def	data.frame containing the modality ID, corresponding layer in BN and maximal number of parents from given layer to GE nodes.
TFtargs	matrix containing the direct interactions between TFs (columns) and their targets (rows).
annot	named list containing the associated methylation probes of given gene.
lm_METH	logical asking whether to use linear regression to filter methylation data (default=TRUE).
r_squared_thres	numeric vector to define the R^2 used as a threshold of significance in linear regression if lm_METH=TRUE (default=0.3).
p_val_thres	numeric vector to define the p-value used as a threshold of significance in linear regression if lm_METH=TRUE (default=0.05).
TFBS_belief	numeric vector to define the belief concerning the TF and its target interaction (default=0.75).
nonGE_belief	numeric vector to define the belief concerning interactions of features except GE-GE (default=0.5).
woPKGE_belief	numeric vector to define the belief concerning GE-GE interactions without prior knowledge (default=0.5).

Value

List of 6 elements needed to init MCMC simulation

Examples

data(list=c("PK", "TFtarg_mat", "annot", "layers_def", "omics"),
package="IntOMICS")
OMICS_mod_res <- OMICS_module(omics = omics, PK = PK, 
    layers_def = layers_def, TFtargs = TFtarg_mat, annot = annot, 
    r_squared_thres = 0.3, lm_METH = TRUE)

anna-pacinkova/intomics_package documentation built on Aug. 13, 2022, 11:38 a.m.