LINKER_runPhase2 {TraRe}R Documentation

Phase II : bipartitive graphs generation

Description

Run second phase of the linker method where a bipartitive graph is generated from the phase I output. A bipartite graph is a set of graph nodes decomposed into two disjoint sets such that no two graph nodes within the same set are adjacent.

Usage

LINKER_runPhase2(modules, Data, NrCores, mode = "VBSR", alpha = 1 - 1e-06)

Arguments

modules

Modules obtained from the phase I linker output.

Data

Matrix of log-normalized estimated counts of the gene expression data (Nr Genes x Nr samples)

NrCores

Nr of computer cores for the parallel parts of the method. Note that the parallelization is NOT initialized in any of the functions. By default, 2.

mode

Chosen method(s) to link module eigengenes to regulators. The available options are 'VBSR', 'LASSOmin', 'LASSO1se' and 'LM'. By default, all methods are chosen.

alpha

alpha parameter if a LASSO model is chosen.

Value

igraph object containing the related drivers and targets in the form of a bipartitive graph.

Examples


   ## We are going to proceed in the same manner as in the `liner_runphaseone()` example
   ## but we start at the end of it, loading the output from the example folder.

   phaseone <- readRDS(paste0(system.file('extdata',package='TraRe'),
                              '/linker_phaseone_example.rds'))

   ## We are loading drivers and targets to generate lognorm_est_counts, as we need it
   ## for the phase 2.

   drivers <- readRDS(paste0(system.file('extdata',package='TraRe'),
                                         '/tfs_linker_example.rds'))
   targets <- readRDS(paste0(system.file('extdata',package='TraRe'),
                                         '/targets_linker_example.rds'))

   lognorm_est_counts <- as.matrix(rbind(drivers,targets))

   ## Now we proceed to call `LINKER_runPhase2()`.
   ## We first, we need to extract modules from the `LINKER_runPhase1()` output.

   modules_phaseone<-LINKER_extract_modules(phaseone)

   ## Now we generate the bipartitive graph from the extracted modules


   graph <- LINKER_runPhase2(modules=modules_phaseone,Data=lognorm_est_counts,
                             NrCores=1,mode='LM')



[Package TraRe version 1.1.0 Index]