CuffFeatureSet-class: Class "CuffFeatureSet"

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 for a set of features (genes, isoforms, TSS, CDS).

Objects from the Class

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

Slots

annotation:

Object of class "data.frame" ~~

fpkm:

Object of class "data.frame" ~~

diff:

Object of class "data.frame" ~~

repFpkm:

Object of class "data.frame" ~~

count:

Object of class "data.frame" ~~

genome:

Object of class "character" ~~

Methods

diffData

signature(object = "CuffFeatureSet"): ...

featureNames

signature(object = "CuffFeatureSet"): ...

features

signature(object = "CuffFeatureSet"): ...

fpkmMatrix

signature(object = "CuffFeatureSet"): ...

repFpkmMatrix

signature(object = "CuffFeatureSet"): ...

countMatrix

signature(object = "CuffFeatureSet"): ...

samples

signature(object = "CuffFeatureSet"): ...

length

signature(object = "CuffFeatureSet"): ...

Accessors

annotation

signature(object="CuffFeatureSet"): Access @annotation slot

Note

None.

Author(s)

Loyal A. Goff

References

None.

See Also

CuffGeneSet

Examples

showClass("CuffFeatureSet")

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