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(dt4rtn)

    # select 5 regulatoryElements for a quick demonstration!
    tfs4test <- dt4rtn$tfs[c("PTTG1","E2F2","FOXM1","E2F3","RUNX2")]

    ## Not run:

    # preprocessing
    rtni <- tni.constructor(expData=dt4rtn$gexp, regulatoryElements=tfs4test,
            rowAnnotation=dt4rtn$gexpIDs)

    # permutation analysis (infers the reference/relevance network)
    rtni<-tni.permutation(rtni, nPermutations=100)

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

    ## End(Not run)

[Package RTN version 2.6.3 Index]