MethylSet instances

Description

This class holds preprocessed data for Illumina methylation microarrays.

Usage

## Constructor

MethylSet(Meth, Unmeth, phenoData, annotation = NULL)

## Data extraction / Accessors

## S4 method for signature 'MethylSet'
getMeth(object)
## S4 method for signature 'MethylSet'
getUnmeth(object)
## S4 method for signature 'MethylSet'
getBeta(object, type = "", offset = 0, betaThreshold = 0)
## S4 method for signature 'MethylSet'
getM(object, type = "", ...)
## S4 method for signature 'MethylSet'
getCN(object, ...)
## S4 method for signature 'MethylSet'
getManifest(object)
## S4 method for signature 'MethylSet'
preprocessMethod(object)

## Utilities
dropMethylationLoci(object, dropRS = TRUE, dropCH = TRUE)

Arguments

Details

This class inherits from eSet. Essentially the class is a representation of a Meth matrix and a Unmeth matrix linked to a pData data frame.

In addition, an annotation and a preprocessMethod slot is present. The annotation slot describes the type of array and also which annotation package to use. The preprocessMethod slot describes the kind of preprocessing that resulted in this dataset.

A MethylSet stores meth and Unmeth. From these it is easy to compute Beta values, defined as

Beta = Meth / (Meth + Unmeth + offset)

The offset is chosen to avoid dividing with small values. Illumina uses a default of 100. M-values (an unfortunate bad name) are defined as

M = logit(Beta) = log( Meth / Unmeth )

This formula has problems if either Meth or Unmeth is zero. For this reason, we can use betaThreshold to make sure Beta is neither 0 nor 1, before taken the logit. What makes sense for the offset and betaThreshold depends crucially on how the data was preprocessed. Do not expect the default values to be particular good.

Constructor

Instances are constructed using the MethylSet function with the arguments outlined above.

Accessors

In the following code, object is a MethylSet.

getMeth(object), getUnmeth(object)

Get the Meth or the Unmeth matrix

getBeta(object)

Get Beta, see details.

getM(object)

get M-values, see details.

getCN(object)

get copy number values which are defined as the sum of the methylation and unmethylation channel.

getManifest(object)

get the manifest associated with the object.

preprocessMethod(object)

Get the preprocess method character.

Utilities

In the following code, object is a MethylSet.

dropMethylationLoci(object)

A unifed interface to removing methylation loci. You can drop SNP probes (probes that measure SNPs, not probes containing SNPs) or CH probes (non-CpG methylation).

Author(s)

Kasper Daniel Hansen khansen@jhsph.edu

See Also

eSet for the basic class structure. Objects of this class are typically created from an RGChannelSet using preprocessRaw or another preprocessing function.

Examples

  showClass("MethylSet")

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 '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(minfi)
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: Biobase
Welcome to Bioconductor

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

Loading required package: lattice
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: SummarizedExperiment
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/minfi/MethylSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MethylSet-class
> ### Title: MethylSet instances
> ### Aliases: MethylSet-class MethylSet getMeth getUnmeth getBeta getM
> ###   preprocessMethod getMeth,MethylSet-method getUnmeth,MethylSet-method
> ###   getBeta,MethylSet-method getM,MethylSet-method getCN,MethylSet-method
> ###   preprocessMethod,MethylSet-method getManifest,MethylSet-method
> ###   show,MethylSet-method initialize,MethylSet-method dropMethylationLoci
> 
> ### ** Examples
> 
>   showClass("MethylSet")
Class "MethylSet" [package "minfi"]

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

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