CuffGene-class: Class "CuffGene"

In cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

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")

cummeRbund documentation built on Nov. 8, 2020, 7:53 p.m.