Class "CuffFeatureSet"

Description

A 'data' container class for all FPKM, annotation, and differential expression data for a set of features (genes, isoforms, TSS, CDS).

Objects from the Class

Objects can be created by calls of the form new("CuffFeatureSet", 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

diffData

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

featureNames

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

features

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

fpkmMatrix

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

repFpkmMatrix

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

countMatrix

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

samples

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

length

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

Accessors

annotation

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

Note

None.

Author(s)

Loyal A. Goff

References

None.

See Also

CuffGeneSet

Examples

showClass("CuffFeatureSet")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

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

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

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