mbrDpiFilter-methods: A filter based on the Data Processing Inequality (DPI)...

Description Usage Arguments Value Examples

Description

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

Usage

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## 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

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data("dt4rtn", package = "RTN")
gexp <- dt4rtn$gexp
annot <- dt4rtn$gexpIDs
tfs1 <- dt4rtn$tfs[c("IRF8","IRF1","PRDM1","AFF3","E2F3")]
tfs2 <- dt4rtn$tfs[c("HCLS1","STAT4","STAT1","LMO4","ZNF552")]
##---mbrPreprocess
rmbr <- mbrPreprocess(gexp=gexp, regulatoryElements1 = tfs1, 
regulatoryElements2=tfs2, gexpIDs=annot)
##---mbrPermutation
rmbr <- mbrPermutation(rmbr, nPermutations=10)
##---mbrBootstrap
rmbr <- mbrBootstrap(rmbr, nBootstrap=10)
##---mbrDpiFilter
rmbr <- mbrDpiFilter(rmbr)

chagasVinicius/RTNduals documentation built on May 13, 2019, 3:10 p.m.