Class "CuffFeature"

Description

A 'data' container class for all FPKM, annotation, and differential expression data for a single feature (gene, isoform, TSS, or CDS).

Objects from the Class

Objects can be created by calls of the form new("CuffFeature", annotation, fpkm, diff, ...).

Slots

annotation:

Object of class "data.frame" ~~

fpkm:

Object of class "data.frame" ~~

diff:

Object of class "data.frame" ~~

repFpkm:

Object of class "data.frame" ~~

count:

Object of class "data.frame" ~~

genome:

Object of class "character" ~~

Methods

fpkmMatrix

signature(object="CuffFeature"): ...

repFpkmMatrix

signature(object = "CuffFeature"): ...

length

signature(x = "CuffFeature"): ...

Accessors

annotation

signature(object="CuffFeature"): Access @annotation slot

diffData

signature(object="CuffFeature"): Access @diff slot

samples

signature(object="CuffFeature"): Get vector of samples

Note

'CuffGene' is a superclass of 'CuffFeature' that links gene information for a given gene with all isoform-, TSS-, and CDS-level data for the given gene.

Author(s)

Loyal A. Goff

References

None

See Also

CuffGene

Examples

showClass("CuffFeature")

Results

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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/CuffFeature-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CuffFeature-class
> ### Title: Class "CuffFeature"
> ### Aliases: CuffFeature-class annotation,CuffFeature-method
> ###   diffData,CuffFeature-method fpkmMatrix,CuffFeature-method
> ###   length,CuffFeature-method samples,CuffFeature-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("CuffFeature")
Class "CuffFeature" [package "cummeRbund"]

Slots:
                                                                        
Name:  annotation       fpkm       diff    repFpkm      count     genome
Class: data.frame data.frame data.frame data.frame data.frame  character

Known Subclasses: "CuffGene"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>