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")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(cummeRbund)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: 'cummeRbund'

The following object is masked from 'package:GenomicRanges':

    promoters

The following object is masked from 'package:IRanges':

    promoters

The following object is masked from 'package:BiocGenerics':

    conditions

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cummeRbund/CuffSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CuffSet-class
> ### Title: Class "CuffSet"
> ### Aliases: CuffSet-class DB genes isoforms TSS CDS promoters splicing
> ###   relCDS conditions varModel DB,CuffSet-method genes,CuffSet-method
> ###   isoforms,CuffSet-method TSS,CuffSet-method CDS,CuffSet-method
> ###   promoters,CuffSet-method splicing,CuffSet-method
> ###   relCDS,CuffSet-method conditions,CuffSet-method
> ###   varModel,CuffSet-method [,CuffSet-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("CuffSet")
Class "CuffSet" [package "cummeRbund"]

Slots:
                                                                          
Name:                DB        phenoData       conditions            genes
Class: SQLiteConnection       data.frame       data.frame         CuffData
                                                                          
Name:          isoforms              TSS              CDS        promoters
Class:         CuffData         CuffData         CuffData         CuffDist
                                        
Name:          splicing           relCDS
Class:         CuffDist         CuffDist
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>