tni2tna.preprocess {RTN} | R Documentation

## A preprocessing function for objects of class TNI.

### 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)

[Package RTN version 2.14.1 Index]