tni.constructor {RTN} | R Documentation

## A constructor for objects of class TNI.

### Description

This function is the main entry point of the TNI pipeline.

### Usage

    tni.constructor(expData, regulatoryElements, rowAnnotation=NULL,
    colAnnotation=NULL, cvfilter=FALSE, verbose=TRUE)

### Arguments

`expData` | a gene expression matrix or 'SummarizedExperiment' object.
`regulatoryElements` | a vector of regulatory elements (e.g. transcription factors).
`rowAnnotation` | an optional data frame with gene annotation. Column 1 must provide all ids listed in the gene expression matrix. Ideally, col1 = <ID>, col2 = <GENEID>, and col3 = <SYMBOL>. Additional annotation can be included in the data frame and will be passed to the resulting TNI object. Furthermore, in order to eventually use the TNI object in `AVS-class` methods, it should also include chromosome coordinates: columns <CHROM>, <START> and <END>. Values in <CHROM> should be listed in [chr1, chr2, chr3, ..., chrX], while <START> and <END> correspond to chromosome positions (see `avs.evse`).
`colAnnotation` | an optional data frame with sample annotation.
`cvfilter` | a single logical value specifying to remove duplicated genes in the gene expression matrix using the probe-to-gene annotation. In this case, 'rowAnnotation' must be provided, with col1 = <ID> and col2 = <GENEID>. Genes duplicated in col2 will be collapsed; the decision is made based on the maximum dinamic range (i.e. keeping the gene with max coefficient of variation across all samples).
`verbose` | a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

### Value

A pre-processed TNI-class object.

### Author(s)

Mauro Castro

### See Also

`TNI-class`

### Examples

    data(tniData)

    #--- run constructor
    rtni <- tni.constructor(expData=tniData$expData,
            regulatoryElements=c("PTTG1","E2F2","FOXM1","E2F3","RUNX2"),
            rowAnnotation=tniData$rowAnnotation)

[Package RTN version 2.11.5 Index]