mbrPermutation,MBR-method {RTNduals}R Documentation

Inference of transcriptional networks.

Description

This function takes an MBR object and computes two transcriptional networks inferred by mutual information (with multiple hypothesis testing corrections).

Usage

## S4 method for signature 'MBR'
mbrPermutation(object, verbose = TRUE, ...)

Arguments

object

A preprocessed object of class MBR.

verbose

A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

...

Additional arguments passed on to the tni.permutation function.

Value

An MBR object with two mutual information matrices, one in each "TNI" slot.

Examples

##--- load a dataset for demonstration
data("dt4rtn", package = "RTN")
gexp <- dt4rtn$gexp
annot <- dt4rtn$gexpIDs
tfs <- dt4rtn$tfs[c("IRF8","IRF1","PRDM1","AFF3","E2F3")]

##--- run mbrPreprocess
rmbr <- mbrPreprocess(gexp=gexp, regulatoryElements = tfs, 
rowAnnotation=annot)

##--- run mbrPermutation(set nPermutations>=1000)
rmbr <- mbrPermutation(rmbr, nPermutations=10)


[Package RTNduals version 1.4.4 Index]