Class "ACMESet"

Description

An extension of ExpressionSet to deal with ACME data including chromosome locations

Objects from the Class

Objects can be created by calls of the form new("ACMESet", assayData, phenoData, featureData, experimentData, annotation, exprs, ...). The exprs assayDataElement stores the data. The featureData slot stores the chromosome location. In practice, the data.frame underlying the featureData MUST contain three columns named chromosome, start, and end; this is enforced by the class validity method.

Slots

assayData:

Object of class "AssayData". See ExpressionSet for details.

phenoData:

Object of class "AnnotatedDataFrame" See ExpressionSet for details.

featureData:

Object of class "AnnotatedDataFrame" See ExpressionSet for details.

experimentData:

Object of class "MIAME" See ExpressionSet for details.

annotation:

Object of class "character" See ExpressionSet for details.

.__classVersion__:

Object of class "Versions" See ExpressionSet for details.

Extends

Class "ExpressionSet", directly. Class "eSet", by class "ExpressionSet", distance 2. Class "VersionedBiobase", by class "ExpressionSet", distance 3. Class "Versioned", by class "ExpressionSet", distance 4.

Methods

chromosome

signature(object = "ACMESet"): Accessor for the chromosome. Returns a vector of chromosomes.

end

signature(x = "ACMESet"): Accessor for the end location for a probe. If that is not known, this could be set to the same value as the start location.

plot

signature(x = "ACMESet"): A convenience plotting method that takes a sample name and chrom as well.

start

signature(x = "ACMESet"): Accessor for the start location for a probe.

Author(s)

Sean Davis <sdavis2@mail.nih.gov>

See Also

ExpressionSet, ACMECalcSet

Examples

showClass("ACMESet")
data(example.agff)
example.agff
head(chromosome(example.agff))
head(start(example.agff))
head(end(example.agff))

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)

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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(ACME)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ACME/ACMESet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ACMESet-class
> ### Title: Class "ACMESet"
> ### Aliases: ACMESet-class chromosome,ACMESet-method end,ACMESet-method
> ###   plot,ACMESet-method start,ACMESet-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("ACMESet")
Class "ACMESet" [package "ACME"]

Slots:
                                                               
Name:      experimentData          assayData          phenoData
Class:              MIAME          AssayData AnnotatedDataFrame
                                                               
Name:         featureData         annotation       protocolData
Class: AnnotatedDataFrame          character AnnotatedDataFrame
                         
Name:   .__classVersion__
Class:           Versions

Extends: 
Class "ExpressionSet", directly
Class "eSet", by class "ExpressionSet", distance 2
Class "VersionedBiobase", by class "ExpressionSet", distance 3
Class "Versioned", by class "ExpressionSet", distance 4

Known Subclasses: "ACMECalcSet"
> data(example.agff)
> example.agff
ACMESet (storageMode: lockedEnvironment)
assayData: 190181 features, 2 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: testsamp1 testsamp2
  varLabels: fullfnames
  varMetadata: labelDescription
featureData
  featureNames: 74065 74066 ... 103913 (190181 total)
  fvarLabels: chromosome source ... comment (8 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> head(chromosome(example.agff))
[1] chr1 chr1 chr1 chr1 chr1 chr1
23 Levels: chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 ... chrX
> head(start(example.agff))
[1] 18370933 18371069 18371199 18371270 18371607 18371703
> head(end(example.agff))
[1] 18371002 18371138 18371268 18371339 18371676 18371772
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>