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 1.2.0 Index]