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")