Class "CuffGene"

Description

A 'data' container class for all FPKM, annotation, and differential expression Data (as well as for all linked features) for a given gene.

Objects from the Class

Objects can be created by calls of the form new("CuffGene", id, isoforms, TSS, CDS, promoters, splicing, relCDS, annotation, fpkm, diff, ...).

Slots

id:

Object of class "character" ~~

isoforms:

Object of class "CuffFeature" ~~

TSS:

Object of class "CuffFeature" ~~

CDS:

Object of class "CuffFeature" ~~

promoters:

Object of class "CuffFeature" ~~

relCDS:

Object of class "CuffFeature" ~~

splicing:

Object of class "CuffFeature" ~~

annotation:

Object of class "data.frame" ~~

genome:

Object of class "character" ~~

fpkm:

Object of class "data.frame" ~~

diff:

Object of class "data.frame" ~~

features:

Object of class "data.frame" ~~

Extends

Class "CuffFeature", directly.

Methods

length

signature(object="CuffFeature"): Part of length validation (internal use only)

makeGeneRegionTrack

signature(object="CuffFeature"): Creates a GeneRegionTrack object (see package Gviz) from a CuffGene object.

genePlot

signature(object="CuffFeature"): Internal use only.

csPie

signature(object="CuffGene"): Allows for visualization of relative isoform proportion as a pie chart by condition (or optionally as stacked bar charts by adding + coord_cartesian()

Accessors

genes

signature(object = "CuffGene"): Access @genes slot

isoforms

signature(object = "CuffGene"): Access @isoforms slot

TSS

signature(object = "CuffGene"): Access @TSS slot

CDS

signature(object = "CuffGene"): Access @CDS slot

promoters

signature(object = "CuffGene"): Access @CDS slot

relCDS

signature(object = "CuffGene"): Access @CDS slot

splicing

signature(object = "CuffGene"): Access @CDS slot

features

signature(object = "CuffGene"): Access @features slot

Note

None.

Author(s)

Loyal A. Goff

References

None.

See Also

CuffFeature

Examples

showClass("CuffGene")

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/CuffGene-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CuffGene-class
> ### Title: Class "CuffGene"
> ### Aliases: CuffGene-class genes,CuffGene-method isoforms,CuffGene-method
> ###   TSS,CuffGene-method CDS,CuffGene-method promoters,CuffGene-method
> ###   relCDS,CuffGene-method splicing,CuffGene-method
> ###   length,CuffGene-method makeGeneRegionTrack
> ###   makeGeneRegionTrack,CuffGene-method genePlot genePlot,CuffGene-method
> ###   csPie csPie,CuffGene-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("CuffGene")
Class "CuffGene" [package "cummeRbund"]

Slots:
                                                                              
Name:           id    features    isoforms         TSS         CDS   promoters
Class:   character  data.frame CuffFeature CuffFeature CuffFeature CuffFeature
                                                                              
Name:     splicing      relCDS  annotation        fpkm        diff     repFpkm
Class: CuffFeature CuffFeature  data.frame  data.frame  data.frame  data.frame
                              
Name:        count      genome
Class:  data.frame   character

Extends: "CuffFeature"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>