get.SJAracne.network: Read SJARACNe Network Result and Return it as List Object

In jyyulab/NetBID: Network-based Bayesian Inference of Drivers, version 2

Read SJARACNe Network Result and Return it as List Object

Description

get.SJAracne.network reads SJARACNe network construction result and returns a list object with network data frame, driver-to-target list and igraph object wrapped inside.

Usage

get.SJAracne.network(network_file = NULL)

Arguments

network_file

character, the path for storing network file. For the output of SJAracne, the name of the network file will be "consensus_network_ncol_.txt" under the output directory.

Details

In the demo, "consensus_network_ncol_.txt" file will be read and convert into a list object. This list contains three elements, network_data, target_list and igraph_obj. network_dat is a data.frame, contains all the information of the network SJARACNe constructed. target_list is a driver-to-target list object. Please check details in get_net2target_list. igraph_obj is an igraph object used to save this directed and weighted network. Each edge of the network has two attributes, weight and sign. weight is the "MI (mutual information)" value and sign is the sign of the spearman correlation coefficient (1, positive regulation; -1, negative regulation).

Value

Return a list containing three elements, network_dat, target_list and igraph_obj.

Examples

if(exists('analysis.par')==TRUE) rm(analysis.par)
network.dir <- sprintf('%s/demo1/network/',system.file(package = "NetBID2")) # use demo
network.project.name <- 'project_2019-02-14' # demo project name
project_main_dir <- 'test/'
project_name <- 'test_driver'
analysis.par  <- NetBID.analysis.dir.create(project_main_dir=project_main_dir,
                                            project_name=project_name,
                                            network_dir=network.dir,
                                            network_project_name=network.project.name)
analysis.par$tf.network  <- get.SJAracne.network(network_file=analysis.par$tf.network.file)
analysis.par$sig.network <- get.SJAracne.network(network_file=analysis.par$sig.network.file)

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jyyulab/NetBID documentation built on Dec. 23, 2024, 6:34 a.m.