alpaca: Main ALPACA function

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Main ALPACA function

Description

This function compares two networks and finds the sets of nodes that best characterize the change in modular structure

Usage

alpaca(net.table, file.stem, verbose = FALSE)

Arguments

net.table	A table of edges, with the first column representing the TFs ("from" nodes) and the second column representing the targets ("to" nodes). The third column contains the edge weights corresponding to the control or healthy network, and the fourth column contains the edge weights for the disease network or network of interest.
file.stem	The folder location and title under which all results will be stored.
verbose	Indicates whether the full differential modularity matrix should also be written to a file. Defaults to FALSE. modularity

Value

List where first element is the membership vector and second element is the contribution score of each node to its module's total differential modularity

Examples

example_path <- system.file("extdata", "Example_2comm.txt", 
package = "netZooR", mustWork = TRUE)
simp.mat <- read.table(example_path,header=TRUE) 
simp.alp <- alpaca(simp.mat,NULL,verbose=FALSE)

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.