tni.get {RTN} | R Documentation |
Get information from individual slots in a TNI object and any available results from a previous analysis.
tni.get(object, what="summary", order=TRUE, ntop=NULL, reportNames=TRUE, idkey=NULL)
object |
an object of class 'TNI' |
what |
a single character value specifying which information should be retrieved from the slots. Options: 'gexp', 'regulatoryElements', 'para', 'refnet', 'tnet','refregulons','regulons','cdt', 'summary', 'annotation' and 'status'. Regulons can also be retrieved mapped to the assiged mode of action ('regulons.and.mode', 'refregulons.and.mode'). |
order |
a single logical value specifying whether or not the output data should be ordered by significance. Valid only for 'cdt' option. |
ntop |
a single integer value specifying to select how many results of top significance from 'cdt' option. |
reportNames |
a single logical value specifying to report regulators with 'names' (when reportNames=TRUE) or not (when reportNames=FALSE). This option takes effect on 'cdt' option if regulators are named with alternative identifiers. |
idkey |
an optional single character value specifying an ID name from the available 'TNI' annotation to be used as alias for data query outputs (obs. it has no effect on consolidated tables). |
get the slot content from an object of class 'TNI' TNI-class
.
Mauro Castro
data(dt4rtn) # select 5 regulatoryElements for a quick demonstration! tfs4test <- dt4rtn$tfs[c("PTTG1","E2F2","FOXM1","E2F3","RUNX2")] ## Not run: rtni <- tni.constructor(expData=dt4rtn$gexp, regulatoryElements=tfs4test, rowAnnotation=dt4rtn$gexpIDs) rtni<-tni.permutation(rtni) rtni<-tni.bootstrap(rtni) rtni<-tni.dpi.filter(rtni) # check summary tni.get(rtni,what="summary") # get reference/relevance network refnet<-tni.get(rtni,what="refnet") # get transcriptional network tnet<-tni.get(rtni,what="tnet") # get status of the pipeline tni.get(rtni,what="status") ## End(Not run)