runrewiring: GRN Modules Rewiring Method.

In ubioinformat/TraRe: Transcriptional Rewiring

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)

gen_heatmap(
  ObjectList,
  module_membership_list,
  allstats,
  imgdir,
  outdir,
  indexpageinfo,
  cmp = FALSE,
  modmeth = "",
  i = 0
)

rawsummary(
  indexpageinfo,
  rawrunmoddata,
  rawsumm,
  lognorm_est_counts,
  outdir,
  foldername_p,
  modmeth,
  exception = FALSE
)

Arguments

ObjectList	Output from preparerewiring()containing some required parameters.
module_membership_list	hash list containing the pair module-significance from the rewiring test.
allstats	array containing information about module's rewiring.
imgdir	path to image directory.
outdir	path to the output directory.
indexpageinfo	list containing information about index.html page.
cmp	boolean indicating the joint heatmap case.
modmeth	method of evaluation from LINKER_run.
i	integer containing the dupla being evaluated.
rawrunmoddata	list containing regulators and target genes from multiplicity table.
rawsumm	list containing generated graph related information and exception variable.
lognorm_est_counts	gene expression matrix from ObjectList.
foldername_p	path to the current foldername.
exception	boolean to avoid errors from previous generated graphs.

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)

ubioinformat/TraRe documentation built on March 10, 2024, 1:11 a.m.