RTN (version 1.10.0)

tni.get: Get information from individual slots in a TNI object.

Description

Get information from individual slots in a TNI object and any available results from a previous analysis.

Usage

tni.get(object, what="summary", order=TRUE, ntop=NULL, reportNames=TRUE, 
idkey=NULL)

Arguments

object

an object of class 'TNI' TNI-class.

what

a single character value specifying which information should be retrieved from the slots. Options: 'gexp', 'tfs', 'para', 'refnet', 'tnet','refregulons','regulons','cdt', 'summary' and 'status'. Regulons can also be retrieved mapped to the assiged mode of action ('regulons.and.mode' or '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).

Value

get the slot content from an object of class 'TNI' TNI-class.

Examples

data(dt4rtn)

tfs4test<-c("PTTG1","E2F2","FOXM1","E2F3","RUNX2")
rtni <- new("TNI", gexp=dt4rtn$gexp, transcriptionFactors=dt4rtn$tfs[tfs4test])

## Not run: 
# 
# rtni<-tni.preprocess(rtni,gexpIDs=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)