CuffSet-class: Class "CuffSet"

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

Description

A 'pointer' class to connect to, and retrieve data from the SQLite backend database.

Objects from the Class

Objects can be created by calls of the form new("CuffSet", DB, conditions, genes, isoforms, TSS, CDS, promoters, splicing, relCDS, ...). Available methods are primary accessors to retrieve CuffGeneSet or CuffGene objects for manipulation.

Slots

DB:

Object of class "SQLiteConnection" ~~

conditions:

Object of class "data.frame" ~~

genes:

Object of class "CuffData" ~~

isoforms:

Object of class "CuffData" ~~

phenoData:

Object of class "data.frame" ~~

TSS:

Object of class "CuffData" ~~

CDS:

Object of class "CuffData" ~~

promoters:

Object of class "CuffDist" ~~

splicing:

Object of class "CuffDist" ~~

relCDS:

Object of class "CuffDist" ~~

conditions:

Object of class "data.frame" ~~

Methods

[

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

Accessors

DB

signature(object="CuffSet"): Access @DB slot

genes

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

isoforms

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

TSS

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

CDS

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

promoters

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

splicing

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

relCDS

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

varModel

signature(object = "CuffSet"): Access varModel info

Note

None.

Author(s)

Loyal A. Goff

References

None.

See Also

None.

Examples

showClass("CuffSet")

gofflab/cummeRbund-BioC-Bridge documentation built on May 17, 2019, 7:30 a.m.