CuffGeneSet-class: Class "CuffGeneSet"

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 (an associated features) for a given set of genes.

Objects from the Class

Objects can be created by calls of the form new("CuffGeneSet", annotation, fpkm, diff, ...).

Slots

ids:

Object of class "character" ~~

isoforms:

Object of class "CuffFeatureSet" ~~

TSS:

Object of class "CuffFeatureSet" ~~

CDS:

Object of class "CuffFeatureSet" ~~

promoters:

Object of class "CuffFeatureSet" ~~

relCDS:

Object of class "CuffFeatureSet" ~~

splicing:

Object of class "CuffFeatureSet" ~~

annotation:

Object of class "data.frame" ~~

fpkm:

Object of class "data.frame" ~~

diff:

Object of class "data.frame" ~~

Extends

Class "CuffFeatureSet", directly.

Methods

No methods defined with class "CuffGeneSet" in the signature.

Accessors

genes

signature(object = "CuffGeneSet"): Access @genes slot

isoforms

signature(object = "CuffGeneSet"): Access @isoforms slot

TSS

signature(object = "CuffGeneSet"): Access @TSS slot

CDS

signature(object = "CuffGeneSet"): Access @CDS slot

promoters

signature(object = "CuffGeneSet"): Access @promoters slot

relCDS

signature(object = "CuffGeneSet"): Access @relCDS slot

splicing

signature(object = "CuffGeneSet"): Access @splicing slot

Note

None.

Author(s)

Loyal A. Goff

References

None.

See Also

CuffFeatureSet

Examples

showClass("CuffGeneSet")

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