neighborhood_size: Neighborhood size

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

Neighborhood size

Description

neighborhood_size This function is determines number of network structures that can be reached from the current network structure.

Usage

neighborhood_size(net, layers_def, B_prior_mat, omics)

Arguments

net	adajcency matrix of given network.
layers_def	data.frame containing the modality ID, corresponding layer in BN and maximal number of parents from given layer to GE nodes.
B_prior_mat	a biological prior matrix.
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.

Value

Numeric of length 1: neighborhood size

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)
adjacency_matrix <- B$B_prior_mat
adjacency_matrix[,] <- 0
neighborhood_size(net = adjacency_matrix, layers_def = layers_def,
B_prior_mat = B$B_prior_mat, omics = B$omics)

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