mbrPermutation,MBR-method {RTNduals} | R Documentation |
This function takes an MBR object and computes two transcriptional networks inferred by mutual information (with multiple hypothesis testing corrections).
## S4 method for signature 'MBR' mbrPermutation(object, verbose = TRUE, ...)
object |
A preprocessed object of class MBR. |
verbose |
A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE). |
... |
Additional arguments passed on to the
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An MBR object with two mutual information matrices, one in each "TNI" slot.
##--- 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 mbrPreprocess rmbr <- mbrPreprocess(gexp=gexp, regulatoryElements = tfs, rowAnnotation=annot) ##--- run mbrPermutation(set nPermutations>=1000) rmbr <- mbrPermutation(rmbr, nPermutations=10)