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)

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