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("tniData", package = "RTN") tfs <- c("IRF8","IRF1","PRDM1","E2F3","STAT4","LMO4","ZNF552") ##--- construct a tni object rtni <- tni.constructor(tniData$expData, regulatoryElements = tfs, rowAnnotation=tniData$rowAnnotation) ##--- 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)