CuffGene-class {cummeRbund} | R Documentation

## Class "CuffGene"

### Description

A 'data' container class for all FPKM, annotation, and differential expression Data (as well as for all linked features) for a given gene.

### Objects from the Class

Objects can be created by calls of the form `new("CuffGene", id, isoforms, TSS, CDS, promoters, splicing, relCDS, annotation, fpkm, diff, ...)`.

### Slots

`id`:

  Object of class `"character"` ~~

`isoforms`:

  Object of class `"CuffFeature"` ~~

`TSS`:

  Object of class `"CuffFeature"` ~~

`CDS`:

  Object of class `"CuffFeature"` ~~

`promoters`:

  Object of class `"CuffFeature"` ~~

`relCDS`:

  Object of class `"CuffFeature"` ~~

`splicing`:

  Object of class `"CuffFeature"` ~~

`annotation`:

  Object of class `"data.frame"` ~~

`genome`:

  Object of class `"character"` ~~

`fpkm`:

  Object of class `"data.frame"` ~~

`diff`:

  Object of class `"data.frame"` ~~

`features`:

  Object of class `"data.frame"` ~~

### Extends

Class `"CuffFeature"`, directly.

### Methods

length

  `signature(object="CuffFeature")`: Part of length validation (internal use only)

makeGeneRegionTrack

  `signature(object="CuffFeature")`: Creates a GeneRegionTrack object (see package Gviz) from a CuffGene object.

genePlot

  `signature(object="CuffFeature")`: Internal use only.

csPie

  `signature(object="CuffGene")`: Allows for visualization of relative isoform proportion as a pie chart by condition (or optionally as stacked bar charts by adding + coord_cartesian()

### Accessors

genes

  `signature(object = "CuffGene")`: Access @genes slot

isoforms

  `signature(object = "CuffGene")`: Access @isoforms slot

TSS

  `signature(object = "CuffGene")`: Access @TSS slot

CDS

  `signature(object = "CuffGene")`: Access @CDS slot

promoters

  `signature(object = "CuffGene")`: Access @CDS slot

relCDS

  `signature(object = "CuffGene")`: Access @CDS slot

splicing

  `signature(object = "CuffGene")`: Access @CDS slot

features

  `signature(object = "CuffGene")`: Access @features slot

### Note

None.

### Author(s)

Loyal A. Goff

### References

None.

### See Also

`CuffFeature`

### Examples

    showClass("CuffGene")

[Package cummeRbund version 2.24.0 Index]