tni.dpi.filter {RTN}R Documentation

Data Processing Inequality (DPI) filter.

Description

This function takes a TNI object and returns the transcriptional network filtered by the data processing inequality algorithm.

Usage

tni.dpi.filter(object, eps=0, verbose=TRUE)

Arguments

object

a processed object of class 'TNI' TNI-class evaluated by the methods tni.permutation and tni.bootstrap.

eps

a single numeric value specifying the threshold under which ARACNe algorithm should apply the dpi filter (eps>=0). If not available (i.e. eps=NA), then the threshold is estimated from the empirical null distribution computed in the permutation and bootstrap steps. For additional details see aracne.

verbose

a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE)

Value

a mutual information matrix in the slot "results" containing a dpi-filtered transcriptional network, see 'tn.dpi' 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)
        
# permutation analysis (infers the reference/relevance network)
rtni <- tni.permutation(rtni)

# dpi filter (infers the transcriptional network)
rtni <- tni.dpi.filter(rtni)


## End(Not run)
[Package RTN version 2.10.1 Index]