runrewiring {TraRe} | R Documentation |
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.
runrewiring(ObjectList)
ObjectList |
Output from |
It creates a folder (in tempdir() by default) containing the files explained above.
## 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)