| mbrDpiFilter,MBR-method {RTNduals} | R Documentation |
This function takes an MBR object and computes two transcriptional networks filtered by the data processing inequality algorithm.
## S4 method for signature 'MBR' mbrDpiFilter(object, verbose = TRUE, ...)
object |
A processed object of class MBR evaluated by
the methods
|
verbose |
A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE). |
... |
Additional arguments passed to the
|
An MBR object with two DPI-filtered 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)
##--- run mbrBootstrap (set nBootstrap>=100)
rmbr <- mbrBootstrap(rmbr, nBootstrap=10)
##--- run mbrDpiFilter
rmbr <- mbrDpiFilter(rmbr)