runrewiring {TraRe} | R Documentation

## GRN Modules Rewiring Method.

### Description

Gene Regulatory Network modules Rewiring method. It performs a permutation test, (what we call rewiring test) and generates an html report containing a correlation matrix with the higher scores obtained from the rewiring test. This matrix is shown in the way of a heatmap, and its sorted by a hierarchical clustering for better interpretation.

### Usage

    runrewiring(ObjectList)

### Arguments

`ObjectList` | Output from `preparerewiring()`containing some required parameters.

### Value

It creates a folder (in tempdir() by default) containing the files explained above.

### Examples

    ## Lets assume that we have already generated the ObjectList, we will load it from
    ## the folder containing the examples files. After this, it is all straight forward.

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

    ## We are going to create the folder containing
    ## the graphs, reports, etc, and then we are deleting it.
    ## If you want to keep it, do not run the last line.

    ## We are modifying output directory for this example.
    objectlist$outdir <- paste(getwd(),'examplefolder',sep='/')

    runrewiring(ObjectList = objectlist)
    unlink(objectlist$outdir,recursive = TRUE)

[Package TraRe version 1.2.0 Index]