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("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")