TNI-class {RTN} | R Documentation

## Class `"TNI"`: an S4 class for Transcriptional Network Inference.

### Description

This S4 class includes a series of methods to do transcriptional network inference for high-throughput gene expression.

### Slots

`gexp`:

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

`regulatoryElements`:

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

`targetElements`:

  Object of class `"character"`, a vector of target elements (e.g. target genes).

`modulators`:

  Object of class `"char_Or_NULL"`, a vector with modulator identifiers.

`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).

`para`:

  Object of class `"list"`, a list of parameters for transcriptional network inference. These parameters are those listed in the functions `tni.permutation`, `tni.bootstrap` and `tni.dpi.filter`.

`results`:

  Object of class `"list"`, a list of results (see the returned values in the functions `tni.permutation`).

`summary`:

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

`status`:

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

### Methods

tni.preprocess

  `signature(object = "TNI")`: see `tni.preprocess`

tni.permutation

  `signature(object = "TNI")`: see `tni.permutation`

tni.bootstrap

  `signature(object = "TNI")`: see `tni.bootstrap`

tni.dpi.filter

  `signature(object = "TNI")`: see `tni.dpi.filter`

tni.conditional

  `signature(object = "TNI")`: see `tni.conditional`

tni.get

  `signature(object = "TNI")`: see `tni.get`

tni.graph

  `signature(object = "TNI")`: see `tni.graph`

tni.gsea2

  `signature(object = "TNI")`: see `tni.gsea2`

tni.area3

  `signature(object = "TNI")`: see `tni.area3`

tni.regulon.summary

  `signature(object = "TNI")`: see `tni.regulon.summary`

tni.prune

  `signature(object = "TNI")`: see `tni.prune`

tni.replace.samples

  `signature(object = "TNI")`: see `tni.replace.samples`

tni.annotate.regulons

  `signature(object = "TNI")`: see `tni.annotate.regulons`

tni.annotate.samples

  `signature(object = "TNI")`: see `tni.annotate.samples`

tni.overlap.genesets

  `signature(object = "TNI")`: see `tni.overlap.genesets`

tni2tna.preprocess

  `signature(object = "TNI")`: see `tni2tna.preprocess`

tni.sre

  `signature(object = "TNI")`: see `tni.sre`

### Author(s)

Mauro Castro

### See Also

`TNA-class`

### Examples

    ## see 'tni.constructor'!

[Package RTN version 2.16.0 Index]