Class "MethyLumiSet" for containing Illumina methylation data

Description

This class inherits from the MethyLumi class (and therefore, from eSet in Biobase) and is designed to hold both the intensities and the calculated betas, as well as pvalues if present.

Objects from the Class

Objects can be created by calls of the form new("MethyLumiSet", assayData, phenoData, featureData, experimentData, annotation, betas). An object of this type is the main storage class for methylation data from Illumina. Subsetting, etc., works as normal (rows represent genes, columns represent samples). There is also a rudimentary history tracking system that is modeled after that from the lumi package.

Slots

QC:

Object of class "QCDataOrNULL", containing either the MethyLumiQC object or NULL

history:

Object of class "data.frame", containing a running history of transforms to the data contained herein

assayData:

Object of class AssayData

phenoData:

Object of class AnnotatedDataFrame

featureData:

Object of class AnnotatedDataFrame, containing the annotation columns from the Illumina Beadstudio output

experimentData:

Object of class MIAME

annotation:

Object of class "character", not currently used

.__classVersion__:

Object of class "Versions"

protocolData:

Object of class "AnnotatedDataFrame" that contains protocol information, including scan date if available

Extends

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

Methods

[

signature(x = "MethyLumiSet"): subsetting, genes as rows, samples as columns

betas<-

signature(object = "MethyLumiSet", value = "matrix"): Set the assayData slot of the same name

betas

signature(object = "MethyLumiSet"): Get the assayData slot of the same name

boxplot

signature(x = "MethyLumiSet"): boxplot of all sample betas

combine

signature(x = "MethyLumiSet", y = "MethyLumiSet")

corplot

signature(x = "MethyLumiSet")

exprs

signature(object = "MethyLumiSet"): returns m-values

getHistory

signature(object = "MethyLumiSet"): returns a data.frame containing the history for this object

hist

signature(x = "MethyLumiSet"): histogram of the betas for the data

initialize

signature(.Object = "MethyLumiSet")

pairs

signature(x = "MethyLumiSet"): pairs plot of the betas for the object. Note that pairs plots of more than a few samples are not very useful.

plotSampleIntensities

signature(x = "MethyLumiSet"): The intensities as output by the Beadstudio software often show a considerable amount of dye bias. This method shows a graphical example of this dye bias. In short, for each of the Cy3 and Cy5 channels, a cutoff in beta is used to calculate which Cy3 and Cy5 values should be plotted at high-methylation and low-methylation status. Any offset between Cy3 and Cy5 when plotted in this way likely represents dye bias and will lead to biases in the estimate of beta.

QCdata<-

signature(object = "MethyLumiSet", value = "MethyLumiQC"): assign QC data to the QC slot

QCdata

signature(object = "MethyLumiSet"): retrieve the QC data.

show

signature(object = "MethyLumiSet")

methylated<-

signature(object = "MethyLumiSet", value = "matrix"): Set the assayData slot associated with methylated intensity

methylated

signature(object = "MethyLumiSet"): Get the assayData slot associated with methylated intensity

unmethylated<-

signature(object = "MethyLumiSet", value = "matrix"): Set the assayData slot associated with unmethylated intensity

unmethylated

signature(object = "MethyLumiSet"): Get the assayData slot associated with unmethylated intensity

qcplot

signature(object = "MethyLumiSet", what, ...): QC plots of various controltypes

controlTypes

signature(object = "MethyLumiSet"): determine the character vector of control types from the QCdata information

Cy3.N

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

Cy5.N

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

combine27k450k

signature(x = "MethyLumiSet", y = "MethyLumiSet"): ...

controlData

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

controlData<-

signature(object = "MethyLumiSet", value = "MethyLumiQC"): ...

featureFilter

signature(eset = "MethyLumiSet"): ...

intensities.IB

signature(x = "MethyLumiSet", channel = "character"): ...

intensities.IB

signature(x = "MethyLumiSet", channel = "missing"): ...

intensities.M

signature(x = "MethyLumiSet", channel = "character"): ...

intensities.M

signature(x = "MethyLumiSet", channel = "missing"): ...

intensities.OOB.allelic

signature(x = "MethyLumiSet", channel = "character", allele = "character"): ...

intensities.OOB.allelic

signature(x = "MethyLumiSet", channel = "missing", allele = "missing"): ...

intensities.OOB

signature(x = "MethyLumiSet", channel = "character"): ...

intensities.OOB

signature(x = "MethyLumiSet", channel = "missing"): ...

intensities.U

signature(x = "MethyLumiSet", channel = "character"): ...

intensities.U

signature(x = "MethyLumiSet", channel = "missing"): ...

intensitiesByChannel

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

negctls.stderr

signature(object = "MethyLumiSet", channel = "character"): ...

negctls.stderr

signature(object = "MethyLumiSet", channel = "missing"): ...

negctls

signature(object = "MethyLumiSet", channel = "character"): ...

negctls

signature(object = "MethyLumiSet", channel = "missing"): ...

negnorm

signature(object = "MethyLumiSet", channel = "character"): ...

negnorm

signature(object = "MethyLumiSet", channel = "missing"): ...

normctls

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

plotSampleIntensities

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

probeNAs

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

sampleNAs

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

total.intensity

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

varFilter

signature(eset = "MethyLumiSet"): ...

Author(s)

Sean Davis & Tim Triche, Jr.

See Also

methylumiR, normalizeMethyLumiSet, methylumIDAT, MethyLumiQC, eSet

Examples

showClass("MethyLumiSet")

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(methylumi)
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")'.

Loading required package: scales
Loading required package: reshape2
Loading required package: ggplot2
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: FDb.InfiniumMethylation.hg19
Loading required package: GenomicFeatures
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: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: org.Hs.eg.db

Loading required package: minfi
Loading required package: lattice
Loading required package: SummarizedExperiment

Attaching package: 'SummarizedExperiment'

The following object is masked from 'package:matrixStats':

    rowRanges

Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/methylumi/MethyLumiSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MethyLumiSet-class
> ### Title: Class '"MethyLumiSet"' for containing Illumina methylation data
> ### Aliases: MethyLumiSet-class Cy3.N,MethyLumiSet-method
> ###   Cy5.N,MethyLumiSet-method QCdata,MethyLumiSet-method
> ###   QCdata<-,MethyLumiSet [,MethyLumiSet,ANY-method
> ###   betas,MethyLumiSet-method betas<-,MethyLumiSet,matrix-method
> ###   boxplot,MethyLumiSet-method
> ###   combine27k450k,MethyLumiSet,MethyLumiSet-method
> ###   combine,MethyLumiSet,MethyLumiSet-method
> ###   controlData,MethyLumiSet-method controlData<-,MethyLumiSet
> ###   controlTypes,MethyLumiSet-method corplot,MethyLumiSet-method
> ###   exprs,MethyLumiSet-method getHistory,MethyLumiSet-method
> ###   hist,MethyLumiSet-method intensities.IB,MethyLumiSet,character-method
> ###   intensities.IB,MethyLumiSet,missing-method
> ###   intensities.M,MethyLumiSet,character-method
> ###   intensities.M,MethyLumiSet,missing-method
> ###   intensities.OOB.allelic,MethyLumiSet,character,character-method
> ###   intensities.OOB.allelic,MethyLumiSet,missing,missing-method
> ###   intensities.OOB,MethyLumiSet,character-method
> ###   intensities.OOB,MethyLumiSet,missing-method
> ###   intensities.U,MethyLumiSet,character-method
> ###   intensities.U,MethyLumiSet,missing-method
> ###   intensitiesByChannel,MethyLumiSet-method
> ###   methylated,MethyLumiSet-method
> ###   methylated<-,MethyLumiSet,matrix-method
> ###   negctls.stderr,MethyLumiSet,character-method
> ###   negctls.stderr,MethyLumiSet,missing-method
> ###   negctls,MethyLumiSet,character-method
> ###   negctls,MethyLumiSet,missing-method
> ###   negnorm,MethyLumiSet,character-method
> ###   negnorm,MethyLumiSet,missing-method normctls,MethyLumiSet-method
> ###   pairs,MethyLumiSet-method plotSampleIntensities,MethyLumiSet-method
> ###   probeNAs,MethyLumiSet-method qcplot,MethyLumiSet-method
> ###   sampleNAs,MethyLumiSet-method show,MethyLumiSet-method
> ###   total.intensity,MethyLumiSet-method unmethylated,MethyLumiSet-method
> ###   unmethylated<-,MethyLumiSet,matrix-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("MethyLumiSet")
Class "MethyLumiSet" [package "methylumi"]

Slots:
                                                               
Name:                  QC            history          assayData
Class:       QCDataOrNULL         data.frame          AssayData
                                                               
Name:           phenoData        featureData     experimentData
Class: AnnotatedDataFrame AnnotatedDataFrame              MIAxE
                                                               
Name:          annotation       protocolData  .__classVersion__
Class:          character AnnotatedDataFrame           Versions

Extends: 
Class "MethyLumi", directly
Class "methylData", directly
Class "eSet", by class "MethyLumi", distance 2
Class "VersionedBiobase", by class "MethyLumi", distance 3
Class "Versioned", by class "MethyLumi", distance 4
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>