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Last data update: 2014.03.03

R: The base class for storing Illumina Methylation data

MethyLumi-class

R Documentation

The base class for storing Illumina Methylation data

Description

This class inherits from eSet from the Biobase package and is used as a base class for the other two methylumi classes, MethyLumiSet and MethyLumiQC.

Objects from the Class

The MethyLumi class is a virtual class and is not meant to be instantiated. Instead, one should instantiate a MethyLumiSet or a MethyLumiQC object.

Slots

assayData:: Object of class "AssayData"
phenoData:: Object of class "AnnotatedDataFrame"
featureData:: Object of class "AnnotatedDataFrame" that will hold the annotation columns from the Beadstudio output, if they are available.
experimentData:: Object of class "MIAME"
annotation:: Object of class "character"; note that this slot is not currently used, but may be used in the future to store the character name of the annotation package, if available.
.__classVersion__:: Object of class "Versions"

Extends

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

Methods

pvals<-: signature(object = "MethyLumi", value = "matrix"): Set the assayData slot of the same name and stores the P-values from BeadStudio
pvals: signature(object = "MethyLumi"): Get the assayData slot of the same name
betas<-: signature(object = "MethyLumi", value = "matrix"): Set the assayData slot of the same name and represents the methylation values for the samples, analogous to exprs() in gene expression data.
betas: signature(object = "MethyLumi"): Get the assayData slot of the same name
methylated<-: signature(object = "MethyLumi", value = "matrix"): Set the assayData slot that represents the Methylated single-channel signal
methylated: signature(object = "MethyLumi"): Get the assayData slot that represents the Methylated single-channel signal
unmethylated<-: signature(object = "MethyLumi", value = "matrix"): Set the assayData slot that represents the Unmethylated single-channel signal
unmethylated: signature(object = "MethyLumi"): Get the assayData slot that represents the Unmethylated single-channel signal
controlTypes: signature(object = "MethyLumi"

: Find the unique control type beeds in the QCdata slot.

qcplot: signature(object = "MethyLumi",what,...): Plot of QC data. This plot can be useful for diagnosing the problems associated with specific samples or arrays. The value for "what" is one of the control types (which can be found by using controlTypes() on the object.
summary: signature(object = "MethyLumi",...)

: summary method for MethyLumi objects.

Author(s)

Sean Davis <sdavis2@mail.nih.gov>

Examples

## The class structure
showClass("MethyLumi")
## read in some data
## Read in sample information
samps <- read.table(system.file("extdata/samples.txt",
                                package = "methylumi"),sep="\t",header=TRUE)
## Perform the actual data reading
## This is an example of reading data from a 
## Sentrix Array format file (actually two files,
## one for data and one for QC probes)
mldat <- methylumiR(system.file('extdata/exampledata.samples.txt',
        package='methylumi'),
      qcfile=system.file('extdata/exampledata.controls.txt',
        package="methylumi"),
      sampleDescriptions=samps)
mldat
## Get history information
getHistory(mldat)
## Get QC data, which is another eSet-derived object
QCdata(mldat)

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/MethyLumi-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MethyLumi-class
> ### Title: The base class for storing Illumina Methylation data
> ### Aliases: MethyLumi-class methylated<-,MethyLumi,matrix-method
> ###   methylated,MethyLumi-method unmethylated<-,MethyLumi,matrix-method
> ###   unmethylated,MethyLumi-method pvals<-,MethyLumi,matrix-method
> ###   pvals,MethyLumi-method summary,MethyLumi-method
> ###   qcplot,Methylumi-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## The class structure
> showClass("MethyLumi")
Class "MethyLumi" [package "methylumi"]

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

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

Known Subclasses: "MethyLumiQC", "MethyLumiSet"
> ## read in some data
> ## Read in sample information
> samps <- read.table(system.file("extdata/samples.txt",
+                                 package = "methylumi"),sep="\t",header=TRUE)
> ## Perform the actual data reading
> ## This is an example of reading data from a 
> ## Sentrix Array format file (actually two files,
> ## one for data and one for QC probes)
> mldat <- methylumiR(system.file('extdata/exampledata.samples.txt',
+         package='methylumi'),
+       qcfile=system.file('extdata/exampledata.controls.txt',
+         package="methylumi"),
+       sampleDescriptions=samps)
> mldat

Object Information:
MethyLumiSet (storageMode: lockedEnvironment)
assayData: 1536 features, 10 samples 
  element names: Avg_NBEADS, BEAD_STDERR, betas, methylated, pvals, unmethylated 
protocolData: none
phenoData
  sampleNames: M_1 M_2 ... F_10 (10 total)
  varLabels: sampleID SampleLabel Sample Gender
  varMetadata: labelDescription
featureData
  featureNames: AATK_E63_R AATK_P519_R ... ZP3_P220_F (1536 total)
  fvarLabels: TargetID ProbeID ... PRODUCT (17 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
Major Operation History:
            submitted            finished
1 2016-07-06 22:57:15 2016-07-06 22:57:16
                                                                                                                                                                                                            command
1 methylumiR(filename = system.file("extdata/exampledata.samples.txt",     package = "methylumi"), qcfile = system.file("extdata/exampledata.controls.txt",     package = "methylumi"), sampleDescriptions = samps)
> ## Get history information
> getHistory(mldat)
            submitted            finished
1 2016-07-06 22:57:15 2016-07-06 22:57:16
                                                                                                                                                                                                            command
1 methylumiR(filename = system.file("extdata/exampledata.samples.txt",     package = "methylumi"), qcfile = system.file("extdata/exampledata.controls.txt",     package = "methylumi"), sampleDescriptions = samps)
> ## Get QC data, which is another eSet-derived object
> QCdata(mldat)
MethyLumiQC (storageMode: lockedEnvironment)
assayData: 44 features, 10 samples 
  element names: Avg_NBEADS, BEAD_STDERR, methylated, pvals, unmethylated 
protocolData: none
phenoData: none
featureData
  featureNames: ALLELE SPECIFIC EXTENSION ALLELE SPECIFIC EXTENSION.1
    ... SECOND HYBRIDIZATION.5 (44 total)
  fvarLabels: TargetID ProbeID
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>