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 |
what |
a single character value specifying which information should be retrieved from the slots. Options: 'summary', 'status', 'para', 'gexp','regulatoryElements', 'tnet', 'refnet', 'regulons', 'refregulons', 'regulons.and.mode', 'refregulons.and.mode', 'rowAnnotation', 'colAnnotation', 'cdt', 'cdtrev'). |
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). |
Options for the 'what' argument retrieve the following types of information:
A list summarizing parameters and results available in the TNI object (see tni.regulon.summary
for a summary of the network and regulons).
A vector indicating the status of each available method in the pipeline.
A list with the parameters used by each available method in the pipeline.
A gene expression matrix.
A vector of regulatory elements (e.g. transcription factors).
A data matrix with MI values, evaluated by the DPI filter. MI values are computed between regulators and targets, with regulators on cols and targets on rows. Note that signals (+/-) are assigned to the inferred associations in order to represent the 'mode of action', which is derived from Pearson's correlation between regulators and targets.
A data matrix with MI values (not evaluated by the DPI filter). MI values are computed between regulators and targets, with regulators on cols and targets on rows. Note that signals (+/-) are assigned to the inferred associations in order to represent the 'mode of action', which is derived from Pearson's correlation between regulators and targets.
A list with regulons extracted from the 'tnet' data matrix.
A list with regulons extracted from the 'refnet' data matrix.
A list with regulons extracted from the 'tnet' data matrix, including the assiged 'mode of action'.
A list with regulons extracted from the 'refnet' data matrix, including the assiged 'mode of action'.
A data frame with probe-to-gene annotation.
A data frame with sample annotation.
A data frame with results from the tni.conditional
analysis pipeline.
A data frame with the same results as retrieved above (using 'cdt'), but arranged in a different format.
Get the slot content from a TNI-class
object.
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 a data matrix with MI values # (not evaluated by 'tni.dpi.filter') refnet<-tni.get(rtni,what="refnet") # get a data matrix with MI values # (evaluated by 'tni.dpi.filter') tnet<-tni.get(rtni,what="tnet") # get status of the pipeline tni.get(rtni,what="status") ## End(Not run)