Description Usage Arguments Value Examples
This function converts a TNI class objects and into one MBR class object.
1 2 | ## S4 method for signature 'TNI'
tni2mbrPreprocess(tni, regulatoryElements = NULL)
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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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ##--- 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)
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