CuffFeature-class: Class "CuffFeature"

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 single feature (gene, isoform, TSS, or CDS).

Objects from the Class

Objects can be created by calls of the form new("CuffFeature", 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

fpkmMatrix

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

repFpkmMatrix

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

length

signature(x = "CuffFeature"): ...

Accessors

annotation

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

diffData

signature(object="CuffFeature"): Access @diff slot

samples

signature(object="CuffFeature"): Get vector of samples

Note

'CuffGene' is a superclass of 'CuffFeature' that links gene information for a given gene with all isoform-, TSS-, and CDS-level data for the given gene.

Author(s)

Loyal A. Goff

References

None

See Also

CuffGene

Examples

showClass("CuffFeature")

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