TNA-class {RTN} | R Documentation

## Class `"TNA"`: an S4 class for Transcriptional Network Analysis.

### Description

This S4 class includes a series of methods to do enrichment, synergy, shadow and overlap analyses in transcriptional networks.

### Objects from the Class

Objects can be created by calls of the form `new("TNA", referenceNetwork, transcriptionalNetwork, regulatoryElements, phenotype, hits)`.

### Slots

`referenceNetwork`:

  Object of class `"matrix"`, an optional partial co-expression matrix.

`transcriptionalNetwork`:

  Object of class `"matrix"`, a partial co-expression matrix.

`regulatoryElements`:

  Object of class `"char_Or_NULL"`, a vector of regulatory elements (e.g. transcription factors).

`phenotype`:

  Object of class `"num_Or_int"`, a numeric or integer vector of phenotypes named by gene identifiers.

`hits`:

  Object of class `"character"`, a character vector of gene identifiers for those considered as hits.

`gexp`:

  Object of class `"matrix"`, a gene expression matrix.

`rowAnnotation`:

  Object of class `"data.frame"`, a data frame with row annotation (e.g. probe-to-gene information).

`colAnnotation`:

  Object of class `"data.frame"`, a data frame with column annotation (e.g. sample information).

`listOfReferenceRegulons`:

  Object of class `"list"`, a list of regulons derived from the referenceNetwork.

`listOfRegulons`:

  Object of class `"list"`, a list of regulons derived from the transcriptionalNetwork (a 'regulon' is a vector of genes or potential transcription factor targets).

`listOfModulators`:

  Object of class `"list"`, a list of modulators derived from the `tni.conditional` analysis.

`para`:

  Object of class `"list"`, a list of parameters for transcriptional network analysis. These parameters are those listed in the functions `tna.mra`, `tna.overlap`, `tna.gsea1`, `tna.synergy`, `tna.shadow` and `tna.gsea2`.

`results`:

  Object of class `"list"`, a list of results (see return values in the functions `tna.mra`,`tna.gsea1`, `tna.overlap`, `tna.synergy`, `tna.shadow` and `tna.gsea2`)

`summary`:

  Object of class `"list"`, a list of summary information for `transcriptionalNetwork`, `regulatoryElements`, `phenotype`,`listOfRegulons`, `para`, and `results`.

`status`:

  Object of class `"character"`, a character value specifying the status of the TNI object based on the available methods.

### Methods

tna.mra

  `signature(object = "TNA")`: see `tna.mra`

tna.overlap

  `signature(object = "TNA")`: see `tna.overlap`

tna.gsea1

  `signature(object = "TNA")`: see `tna.gsea1`

tna.gsea2

  `signature(object = "TNA")`: see `tna.gsea2`

tna.synergy

  `signature(object = "TNA")`: see `tna.synergy`

tna.shadow

  `signature(object = "TNA")`: see `tna.shadow`

tna.get

  `signature(object = "TNA")`: see `tna.get`

tna.graph

  `signature(object = "TNA")`: see `tna.graph`

### Author(s)

Mauro Castro

### See Also

`TNI-class`. `tni2tna.preprocess`.

### Examples

    ## see 'tni2tna.preprocess' method!

[Package RTN version 2.6.3 Index]