mbrDpiFilter,MBR-method {RTNduals}R Documentation

A filter based on the Data Processing Inequality (DPI) algorithm.

Description

This function takes an MBR object and computes two transcriptional networks filtered by the data processing inequality algorithm.

Usage

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

Arguments

object

A processed object of class MBR evaluated by the methods mbrPermutation and mbrBootstrap.

verbose

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

...

Additional arguments passed to the tni.dpi.filter function.

Value

An MBR object with two DPI-filtered 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)

##--- run mbrBootstrap (set nBootstrap>=100)
rmbr <- mbrBootstrap(rmbr, nBootstrap=10)

##--- run mbrDpiFilter
rmbr <- mbrDpiFilter(rmbr)


[Package RTNduals version 1.4.4 Index]