| mbrPriorEvidenceTable,MBR-method {RTNduals} | R Documentation |
If available, this function adds external evidences to an 'MBR' object.
## S4 method for signature 'MBR' mbrPriorEvidenceTable(object, priorEvidenceTable, evidenceColname, verbose = TRUE)
object |
A processed object of class MBR evaluated by the
method |
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). |
An MBR object with an updated 'data.frame' in the slot 'results' listing the input additional evidences.
##--- 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")