CuffData-class: Class "CuffData"

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

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")

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