tni2tna.preprocess: A preprocessing function for objects of class TNI.

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

Description

This is a generic function.

Usage

tni2tna.preprocess(object, phenotype=NULL, hits=NULL, phenoIDs=NULL, 
duplicateRemoverMethod="max", verbose=TRUE)

Arguments

object	a processed object of class 'TNI' TNI-class evaluated by the methods tni.permutation, tni.bootstrap and tni.dpi.filter.
phenotype	a numeric vector of phenotypes named by gene identifiers (usually log2 differential expression values). Required for the tna.gsea1 and tna.gsea2) methods.
hits	a character vector of gene identifiers for those considered as hits. Required for the tna.mra method.
phenoIDs	an optional 2cols-matrix used to aggregate genes in the 'phenotype' (e.g. probe-to-gene ids; in this case, col 1 should correspond to probe ids).
duplicateRemoverMethod	a single character value specifying the method to remove the duplicates. The current version provides "min" (minimum), "max" (maximum), "average". Further details in 'duplicateRemover' function at the HTSanalyzeR package.
verbose	a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

A pre-processed TNA-class object.

Author(s)

Mauro Castro

See Also

TNI-class TNA-class

Examples

data(tniData)
data(tnaData)

## 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)
rtna <- tni2tna.preprocess(rtni, phenotype=tnaData$phenotype, 
        hits=tnaData$hits, phenoIDs=tnaData$phenoIDs)

## End(Not run)

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