CuffData-class {cummeRbund} | R Documentation

## Class "CuffData"

### Description

A 'pointer' class for all information (FPKM, annotation, differential expression) for a given feature type (genes, isoforms, TSS, CDS). The methods for this function communicate directly with the SQL backend to present data to the user.

### Objects from the Class

Objects can be created by calls of the form `new("CuffData", DB, tables, filters, type, idField, ...)`.

### Slots

`DB`:

  Object of class `"SQLiteConnection"` ~~

`tables`:

  Object of class `"list"` ~~

`filters`:

  Object of class `"list"` ~~

`type`:

  Object of class `"character"` ~~

`idField`:

  Object of class `"character"` ~~

### Methods

dim

  `signature(x = "CuffData")`: ...

getFeatures

  `signature(object = "CuffData")`: ...

DB

  `signature(object = "CuffData")`: Accessor for @DB slot

diffTable

  `signature(object = "CuffData")`: Create a Full table (wide format) of differential expression information for all pairwise comparisons

makeRnk

  `signature(object = "CuffData")`: Internal method to create .rnk file. Should not be called directly

annotation

  `signature(object="CuffData")`: Access annotation data

### Note

None

### Author(s)

Loyal A. Goff

### References

None

### See Also

None

### Examples

    showClass("CuffData")

[Package cummeRbund version 2.36.0 Index]