tni.bootstrap: Inference of consensus transcriptional networks.

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

Description

This function takes a TNI object and returns the consensus transcriptional network.

Usage

tni.bootstrap(object, nBootstraps=100, consensus=95, parChunks=NULL, verbose=TRUE)

Arguments

object	a processed object of class 'TNI' TNI-class evaluated by the method tni.permutation.
nBootstraps	a single integer or numeric value specifying the number of bootstraps for deriving a consensus between every TF-target association inferred in the mutual information analysis. If running in parallel, nBootstraps should be greater and multiple of parChunks.
consensus	a single integer or numeric value specifying the consensus fraction (in percentage) under which a TF-target association is accepted.
parChunks	an optional single integer value specifying the number of bootstrap chunks to be used in the parallel analysis.
verbose	a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE)

Value

a matrix in the slot "results" containing a reference transcriptional network, see 'tn.ref' option in tni.get.

Author(s)

Mauro Castro

See Also

TNI-class

Examples

data(tniData)

## Not run: 

# preprocessing
rtni <- tni.constructor(expData=tniData$expData, 
        regulatoryElements=c("PTTG1","E2F2","FOXM1","E2F3","RUNX2"), 
        rowAnnotation=tniData$rowAnnotation)

# linear version!
rtni <- tni.permutation(rtni)
rtni <- tni.bootstrap(rtni)

## parallel version with SNOW package!
#library(snow)
#options(cluster=snow::makeCluster(3, "SOCK"))
#rtni <- tni.permutation(rtni)
#rtni <- tni.bootstrap(rtni)
#stopCluster(getOption("cluster"))

## End(Not run)

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