mbrGet,MBR-method {RTNduals} | R Documentation |
Get information from individual slots in an MBR object and any available results from previous analysis.
## S4 method for signature 'MBR' mbrGet(object, what = "status")
object |
A preprocessed object of class MBR |
what |
a single character value specifying which information should be retrieved from the slots. Options: "TNI", "regulatoryElements", "dualRegulons", "results", "para", "summary", "status", "dualsCorrelation", "dualsOverlap", and "dualsCorMatrix" |
Content from slots in the MBR object
##--- load a dataset for demonstration data("tniData", package = "RTN") gexp <- tniData$expData annot <- tniData$rowAnnotation tfs <- c("IRF8","IRF1","PRDM1","E2F3","STAT4","LMO4","ZNF552") ##--- 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) ##--- get the 'TNI' slot using 'mbrGet' tni <- mbrGet(rmbr, what="TNI")