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")

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/CuffData-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CuffData-class
> ### Title: Class "CuffData"
> ### Aliases: CuffData-class dim,CuffData-method getFeatures,CuffData-method
> ###   DB,CuffData-method makeRnk makeRnk,CuffData-method
> ###   annotation,CuffData-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("CuffData")
Class "CuffData" [package "cummeRbund"]

Slots:
                                                                          
Name:                DB           tables          filters             type
Class: SQLiteConnection             list             list        character
                       
Name:           idField
Class:        character
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>