fan_in_reverse: Number of reverse edge candidates

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

Number of reverse edge candidates

Description

fan_in_reverse Determine the number of edges that can be reversed using the fan-in restriction in the largest layer.

Usage

fan_in_reverse(positions, net_layer_max, layers_def)

Arguments

positions	character vector indicating the interaction between two nodes (the first string indicates the source node, the second string indicates the target node).
net_layer_max	adjacency matrix of the network containing only GE nodes.
layers_def	data.frame containing the modality ID, corresponding layer in BN and maximal number of parents from given layer to GE nodes.

Value

Numeric vector of length 1: reverse edge candidates

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$B_prior_mat
adjacency_matrix[,] <- 0
adjacency_matrix[1,2] <- 1
layer_max <- colnames(B$omics[[layers_def$omics[1]]])
fan_in_reverse(positions = c(row=1,col=2), 
net_layer_max = adjacency_matrix[layer_max,layer_max], 
layers_def = layers_def)

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