| tni2mbrPreprocess,TNI-method {RTNduals} | R Documentation |
This function converts a TNI class objects and into one MBR class object.
## S4 method for signature 'TNI' tni2mbrPreprocess(tni, regulatoryElements = NULL)
tni |
A 'TNI' class object. |
regulatoryElements |
An optional character vector specifying which 'TNI' regulatory elements should be evaluated. If 'NULL' all regulatory elements will be evaluated. |
An MBR object.
##--- load a dataset for demonstration
data("dt4rtn", package = "RTN")
gexp <- dt4rtn$gexp
annot <- dt4rtn$gexpIDs
tfs <- dt4rtn$tfs[c("IRF8","IRF1","PRDM1","AFF3","E2F3")]
##--- 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)