tni2mbrPreprocess,TNI-method {RTNduals}R Documentation

A preprocessing function for objects of class MBR.

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("dt4rtn", package = "RTN")
gexp <- dt4rtn$gexp
annot <- dt4rtn$gexpIDs
tfs <- dt4rtn$tfs[c("IRF8","IRF1","PRDM1","AFF3","E2F3")]

##--- construct a tni object
rtni <- tni.constructor(gexp, regulatoryElements = tfs, rowAnnotation=annot)

##--- 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)


[Package RTNduals version 1.6.2 Index]