rewiring_regulon_level: Perform the rewiring at the regulon level

In ubioinformat/TraRe: Transcriptional Rewiring

Perform the rewiring at the regulon level

Description

Perform the rewiring test to regulons using a hypergeometric test.

Usage

rewiring_regulon_level(
  linker_output,
  TraReObj,
  fpath = "",
  rewired = TRUE,
  final_signif_thresh = 0.05,
  outdir = tempdir()
)

Arguments

linker_output	Output from LINKER_run function (recommended with 50 bootstraps).
TraReObj	the TrareObj generated during preprocessing step before GRN inference.
fpath	Path of the output file from rewired_gene_level function with rewired modules list.
rewired	Bool indicating whether the analysis is to be done regulons from rewired modules (default= TRUE)
final_signif_thresh	Significance threshold for the rewiring method. The lower the threshold, the more restrictive the method. Default set to 0.05.
outdir	Directory for the output folder to be located (default: tempdir()).

Value

Return an object list with a data.frame for each regulon with filtered targets by pvalue, multiplicity and the igraph object.

Examples

## We will be using an output file we generated with LINKER_run and the 
## same expression datainput  object.

## linker_output <- readRDS(paste0(system.file('extdata',package='TraRe'),
##                                     'linkeroutput_rewiring_example.rds'))

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

## Add the phenotype to TraReObj if it was not before.
## TraReObj <- rewiring_add_phenotype(TraReObj, phenotype)

## Select directory for output file
## outdir <- system.file('extdata',package='TraRe')
## regulons <- rewiring_regulon_level(linker_output = linker_output, 
##                                    TraReObj = TraReObj,
##                                    rewired = TRUE,
##                                    final_signif_thresh = 0.05,
##                                    outdir = outdir)

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