tna.overlap {RTN} | R Documentation

## Overlap analysis over a list of regulons.

### Description

This function takes a TNA object and returns the results of the overlap analysis among regulons in a transcriptional network (with multiple hypothesis testing corrections).

### Usage

    tna.overlap(object, pValueCutoff=0.05, pAdjustMethod="BH", minRegulonSize=15, tnet="ref",
                tfs=NULL, verbose=TRUE)

### Arguments

`object` | a preprocessed object of class 'TNA' `TNA-class`.
`pValueCutoff` | a single numeric value specifying the cutoff for p-values considered significant.
`pAdjustMethod` | a single character value specifying the p-value adjustment method to be used (see 'p.adjust' for details).
`minRegulonSize` | a single integer or numeric value specifying the minimum number of elements in a regulon that must map to elements of the gene universe. Gene sets with fewer than this number are removed from the analysis.
`tnet` | a single character value specifying which transcriptional network should to used to compute the overlap analysis. Options: "dpi" and "ref".
`tfs` | an optional vector with transcription factor identifiers.
`verbose` | a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

### Value

a data frame in the slot "results", see 'overlap' option in `tna.get`.

### Author(s)

Mauro Castro

### See Also

`TNA-class`

### Examples

    data(dt4rtn)

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

    ## Not run:

    rtni <- tni.constructor(expData=dt4rtn$gexp, regulatoryElements=tfs4test,
            rowAnnotation=dt4rtn$gexpIDs)
    rtni<-tni.permutation(rtni)
    rtni<-tni.bootstrap(rtni)
    rtni<-tni.dpi.filter(rtni)
    rtna<-tni2tna.preprocess(rtni, phenotype=dt4rtn$pheno, hits=dt4rtn$hits, phenoIDs=dt4rtn$phenoIDs)

    #run overlap analysis pipeline
    rtna <- tna.overlap(rtna)

    #get results
    tna.get(rtna,what="overlap")

    ## End(Not run)

[Package RTN version 2.6.3 Index]