CuffSet-class {cummeRbund} | R Documentation

## Class "CuffSet"

### 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")

[Package cummeRbund version 2.22.0 Index]