pf_UB_est: Partition function upper bound

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

Partition function upper bound

Description

pf_UB_est Partition function upper bound estimation with beta = 0. For each node returns energy over all possible parent set configurations and BGe score.

Usage

pf_UB_est(omics, B_prior_mat, layers_def, annot)

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.
B_prior_mat	a biological prior matrix.
layers_def	data.frame containing the modality ID, corresponding layer in BN and maximal number of parents from given layer to GE nodes.
annot	named list containing the associated methylation probes of given gene.

Value

List of 4 elements needed to simulate MCMC sampling

Examples

data(list=c("PK", "TFtarg_mat", "annot", "layers_def", "omics"),
package="IntOMICS")
B <- B_prior_mat(omics = omics, PK = PK, layers_def = layers_def, 
     annot = annot, lm_METH = TRUE, r_squared_thres = 0.3,
     p_val_thres = 0.05, TFtargs = TFtarg_mat, TFBS_belief = 0.75, 
     nonGE_belief = 0.5, woPKGE_belief = 0.5)
pf_UB_est(omics = B$omics, B_prior_mat = B$B_prior_mat, 
layers_def = layers_def, annot = B$annot)

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