mbrGet-methods: Get information from individual slots in MBR object.

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

Description

Get information from individual slots in an MBR object and any available results from previous analysis.

Usage

## S4 method for signature 'MBR'
mbrGet(object, what = "status")

Arguments

object	A preprocessed object of class MBR
what	a single character value specifying which information should be retrieved from the slots. Options: "TNI", "regulatoryElements", "dualRegulons", "results", "para", "summary", "status", "dualsCorrelation", "dualsOverlap", and "dualsCorMatrix"

Value

Content from slots in the MBR object

Examples

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

##--- 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)

##--- get the 'TNI' slot using 'mbrGet'
tni <- mbrGet(rmbr, what="TNI")

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