tni.regulon.summary: Summary of regulon characteristics.

In RTN: RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Description

This function takes a TNI object and optionally a list of regulatory elements and returns a summary of the network (if no regulatory elements are given) or of the chosen regulon or regulons.

Usage

tni.regulon.summary(object, regulatoryElements = NULL, verbose = TRUE)

Arguments

object	a preprocessed object of class 'TNI' TNI-class already evaluated by the tni.dpi.filter method.
regulatoryElements	a vector of valid regulatory elements (e.g. transcription factors).
verbose	a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

It returns a print-out of the network summary (if verbose is TRUE) and invisibly returns a data.frame of network characteristics such as regulon size and regulon balance.

Author(s)

Clarice Groeneveld

See Also

TNI-class

Examples

data(tniData)

## Not run: 

rtni <- tni.constructor(expData=tniData$expData, 
        regulatoryElements=c("PTTG1","E2F2","FOXM1","E2F3","RUNX2"), 
        rowAnnotation=tniData$rowAnnotation)
rtni <- tni.permutation(rtni)
rtni <- tni.bootstrap(rtni)
rtni <- tni.dpi.filter(rtni)

# Summary of the network
tni.regulon.summary(rtni)

# Summary of a regulon
tni.regulon.summary(rtni, regulatoryElements = "PTTG1")


## End(Not run)

RTN documentation built on Nov. 12, 2020, 2:02 a.m.