tni2mbrPreprocess-methods: A preprocessing function for objects of class MBR.

In RTNduals: Analysis of co-regulation and inference of 'dual regulons'

Description

This function converts a TNI class objects and into one MBR class object.

Usage

## S4 method for signature 'TNI'
tni2mbrPreprocess(tni, regulatoryElements = NULL)

Arguments

tni	A 'TNI' class object.
regulatoryElements	An optional character vector specifying which 'TNI' regulatory elements should be evaluated. If 'NULL' all regulatory elements will be evaluated.

Value

An MBR object.

Examples

##--- load a dataset for demonstration
data("tniData", package = "RTN")
tfs <- c("IRF8","IRF1","PRDM1","E2F3","STAT4","LMO4","ZNF552")

##--- construct a tni object
rtni <- tni.constructor(tniData$expData, regulatoryElements = tfs, 
rowAnnotation=tniData$rowAnnotation)

##--- compute regulons 
## set nPermutations>=1000
rtni <- tni.permutation(rtni, nPermutations=30)

## set nBootstrap>=100
rtni <- tni.bootstrap(rtni, nBootstrap=30)

## 'eps=NA' estimates threshold from empirical null
rtni <- tni.dpi.filter(rtni, eps=NA)

##--- construct a mbr object
rmbr <- tni2mbrPreprocess(rtni)

RTNduals documentation built on Nov. 12, 2020, 2:03 a.m.