mbrPriorEvidenceTable,MBR-method {RTNduals}R Documentation

Entry point for external evidences.

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

##--- run mbrAssociation (set nPermutations>=1000 and nBootstrap>=100)
rmbr <- mbrPreprocess(gexp=gexp, regulatoryElements = tfs, 
rowAnnotation=annot)
rmbr <- mbrPermutation(rmbr, nPermutations=10)
rmbr <- mbrBootstrap(rmbr, nBootstrap=10)
rmbr <- mbrDpiFilter(rmbr)
rmbr <- mbrAssociation(rmbr, pValueCutoff = 0.05, nPermutations=10)

##--- 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")


[Package RTNduals version 1.4.4 Index]