merge_TF_SIG.AC: Merge Activity Values from TF (transcription factors)...

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

Merge Activity Values from TF (transcription factors) ExpressionSet Object and Sig (signaling factors) ExpressionSet Object

Description

merge_TF_SIG.AC combines the activity value from TF (transcription factors) and Sig (signaling factors) ExpressionSet objects together, and adds "_TF" or "_SIG" suffix to drivers for easier distinction.

Usage

merge_TF_SIG.AC(TF_AC = NULL, SIG_AC = NULL)

Arguments

TF_AC	ExpressionSet object, containing the activity values for all TFs.
SIG_AC	ExpressionSet object, containing the activity values for all SIGs.

Value

Return an ExpressionSet object.

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)
## get eset (here for demo, use network.par$net.eset)
network.par <- list()
network.par$out.dir.DATA <- system.file('demo1','network/DATA/',package = "NetBID2")
NetBID.loadRData(network.par=network.par,step='exp-QC')
analysis.par$cal.eset <- network.par$net.eset
ac_mat_TF <- cal.Activity(target_list=analysis.par$tf.network$target_list,
                       cal_mat=Biobase::exprs(analysis.par$cal.eset),
                       es.method='weightedmean')
ac_mat_SIG <- cal.Activity(target_list=analysis.par$tf.network$target_list,
                       cal_mat=Biobase::exprs(analysis.par$cal.eset),
                       es.method='weightedmean')
analysis.par$ac.tf.eset  <- generate.eset(exp_mat=ac_mat_TF,
                                          phenotype_info=Biobase::pData(analysis.par$cal.eset))
analysis.par$ac.sig.eset <- generate.eset(exp_mat=ac_mat_SIG,
                                          phenotype_info=Biobase::pData(analysis.par$cal.eset))
analysis.par$merge.ac.eset <- merge_TF_SIG.AC(TF_AC=analysis.par$ac.tf.eset,
                                          SIG_AC=analysis.par$ac.sig.eset)

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