mbrPriorEvidenceTable-methods: Entry point for external evidences.

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

Description

If available, this function adds external evidences to an 'MBR' object.

Usage

## S4 method for signature 'MBR'
mbrPriorEvidenceTable(
  object,
  priorEvidenceTable,
  evidenceColname,
  verbose = TRUE
)

Arguments

object	A processed object of class MBR evaluated by the method mbrAssociation.
priorEvidenceTable	An 'data.frame' with three columns representing (1) regulatory elements 1, (2) regulatory elements 2, and (3) external evidences between the regulatory elements.
evidenceColname	A single character value specifying a column in the 'priorEvidenceTable'.
verbose	A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

An MBR object with an updated 'data.frame' in the slot 'results' listing the input additional evidences.

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)

##--- run mbrAssociation 
## set nPermutations>=1000
rmbr <- mbrAssociation(rmbr, pValueCutoff = 0.05, nPermutations=30)

##--- check results
results <- mbrGet(rmbr, what="dualsCorrelation")

##--- add supplementary evidence table
## here we build a 'toy' example using the 'rnorm' function 
## for demonstration purposes only!
priorEvidenceTable <- results[,c("Regulon1","Regulon2")]
priorEvidenceTable$ToyEvidence <- rnorm(nrow(results))
priorEvidenceTable

##--- add supplementary evidences
# rmbr <- mbrPriorEvidenceTable(rmbr, priorEvidenceTable=priorEvidenceTable, evidenceColname = "ToyEvidence")

##--- check updated results
# mbrGet(rmbr, what="dualsCorrelation")

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