Class "MethyLumiM": for Illumina Methylation microarray data using logRatios

Description

MethyLumiM is a class inherited from ExpressionSet-class. It is designed for Illumina Methylation microarray data. The exprs dataMatrix included in the assayData slot of MethyLumiM object includes a matrix of M-values, which is the log2 ratio of methylated and unmethylated probe intensities. The MethyLumiM class include a boxplot function uniquely designed for two-mode histogram data. It also include a coerce function to map from MethyLumi-class, MethyLumiSet-class or other eSet-class inherited object to MethyLumiM class object.

Objects from the Class

Objects can be created by calls of the form new("MethyLumiM", exprs, methylated, unmethylated, detection, methylated.N, unmethylated.N, ..., assayData). The "exprs" is a matrix of M-values, which is the log2 ratio of methylated and unmethylated probe intensities; "methylated" and "unmethylated" are intensity matrix measured by methylated and unmethylalted probes of Illumina Infinium methylation microarray; "detection" is the detection p-value outputted by Illumina GenomeStudio software; "methylated.N" and "unmethylated.N" are bead numbers for methylated and unmethylalted probes. "exprs", "methylated" and "unmethylated" information are required for MethyLumiM class. When creating a new MethyLumiM object, the information of "exprs", "methylated", "unmethylated" and "detection" can also be provided directly through "assayData".

Slots

history:

Object of class "data.frame" recording the operation history of the LumiBatch object.

controlData:

Object of class "MethyLumiQC" to keep the QC probe measurement information.

dataType:

The type of data stored in the "exprs" data matrix in "assayData". It can be "M" (M-value), "Beta" (Beta-value") or "Intensity" (Intensity of CpG-site)

assayData:

Object of class "AssayData", which includes "exprs", "methylated", "unmethylated", "detection", "methylated.N" and "unmethylated.N" data matrix

phenoData:

Object of class "AnnotatedDataFrame", See eSet-class

featureData:

Object of class "AnnotatedDataFrame", See eSet-class

experimentData:

Object of class "MIAME", See eSet-class

annotation:

Object of class "character", See eSet-class

protocolData:

Object of class "AnnotatedDataFrame", See eSet-class

.__classVersion__:

Object of class "Versions", See eSet-class

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

boxplot

signature(x = "MethyLumiM"): plot distribution of M-value

coerce

signature(from = "eSet", to = "MethyLumiM"): map from MethyLumi-class, MethyLumiSet-class or other eSet-class inherited object to MethyLumiM class object. MethyLumiM object will only keep "exprs", "methylated", "unmethylated" and "detection" data matrix in the assayData.

getHistory

signature(object = "MethyLumiM"): access the operation history of MethyLumiM object.

initialize

signature(.Object = "MethyLumiM"): class initialization

methylated

signature(object = "MethyLumiM"): retrieve the data matrix measured by methylated probes

methylated<-

signature(object = "MethyLumiM"): set the data matrix measured by methylated probes

unmethylated

signature(object = "MethyLumiM"): retrieve the data matrix measured by unmethylated probes

unmethylated<-

signature(object = "MethyLumiM"): set the data matrix measured by unmethylated probes

methylated.N

signature(object = "MethyLumiM"): retrieve the data matrix keeping the number of beads of methylated probes

methylated.N<-

signature(object = "MethyLumiM"): set the data matrix keeping the number of beads of methylated probes

unmethylated.N

signature(object = "MethyLumiM"): retrieve the data matrix keeping the number of beads of unmethylated probes

unmethylated.N<-

signature(object = "MethyLumiM"): set the data matrix keeping the number of beads of unmethylated probes

detection

signature(object = "MethyLumiM"): retrieve detection data matrix in AssayData-class

detection<-

signature(object = "MethyLumiM"): set detection data matrix in AssayData-class

controlData

signature(object = "MethyLumiM"): retrieve the controlData in MethyLumiQC-class

controlData<-

signature(object = "MethyLumiM"): set controlData in MethyLumiQC-class

dataType

signature(object = "MethyLumiM"): retrieve the dataType, by default it is "M", it can also be "Beta" or "Intensity"

dataType<-

signature(object = "MethyLumiM"): set dataType in MethyLumiM-class, the value can be "M", "Beta" or "Intensity"

Author(s)

Pan DU

References

1. Du, P., Zhang, X, Huang, C.C., Jafari, N., Kibbe, W.A., Hou, L., and Lin, S.M., (2010) 'Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis'

See Also

MethyLumi-class and MethyLumiSet-class

Examples

showClass("MethyLumiM")

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/MethyLumiM-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MethyLumiM-class
> ### Title: Class "MethyLumiM": for Illumina Methylation microarray data
> ###   using logRatios
> ### Aliases: MethyLumiM-class MethyLumiM QCdata,MethyLumiM-method
> ###   [,MethyLumiM,ANY-method betas,MethyLumiM-method
> ###   combine,MethyLumiM,MethyLumiM-method controlData,MethyLumiM-method
> ###   controlData<-,MethyLumiM,ANY-method controlTypes,MethyLumiM-method
> ###   detection,MethyLumiM-method detection<-,MethyLumiM-method
> ###   getHistory,MethyLumiM-method intensitiesByChannel,MethyLumiM-method
> ###   methylated.N,MethyLumiM-method methylated.N<-,MethyLumiM,ANY-method
> ###   methylated,MethyLumiM-method methylated<-,MethyLumiM,ANY-method
> ###   negctls,MethyLumiM,character-method negctls,MethyLumiM,missing-method
> ###   negnorm,MethyLumiM,character-method negnorm,MethyLumiM,missing-method
> ###   normctls,MethyLumiM-method probeNAs,MethyLumiM-method
> ###   pvals,MethyLumiM-method sampleNAs,MethyLumiM-method
> ###   total.intensity,MethyLumiM-method unmethylated.N,MethyLumiM-method
> ###   unmethylated.N<-,MethyLumiM,ANY-method unmethylated,MethyLumiM-method
> ###   unmethylated<-,MethyLumiM,ANY-method dataType,MethyLumiM-method
> ###   dataType<-,MethyLumiM,ANY-method dataType<-,MethyLumiM-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("MethyLumiM")
Class "MethyLumiM" [package "methylumi"]

Slots:
                                                               
Name:         controlData            history           dataType
Class:       QCDataOrNULL         data.frame          character
                                                               
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 "methylData", directly
Class "eSet", by class "ExpressionSet", distance 2
Class "VersionedBiobase", by class "ExpressionSet", distance 3
Class "Versioned", by class "ExpressionSet", distance 4
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>