MethylSet-class: MethylSet instances

In kasperdanielhansen/minfi: Analyze Illumina Infinium DNA methylation arrays

MethylSet instances

Description

This class holds preprocessed data for Illumina methylation microarrays.

Usage

## Constructor

MethylSet(Meth = new("matrix"), Unmeth = new("matrix"),
          annotation = "", preprocessMethod = "", ...)

## 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)
## S4 method for signature 'MethylSet'
annotation(object)
## S4 method for signature 'MethylSet'
pData(object)
## S4 method for signature 'MethylSet'
sampleNames(object)
## S4 method for signature 'MethylSet'
featureNames(object)

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

Arguments

object	A MethylSet.
Meth	A matrix of methylation values (between zero and infinity) with each row being a methylation loci and each column a sample.
Unmeth	See the Meth argument.
annotation	An annotation string, optional.
preprocessMethod	A character, optional.
type	How are the values calculated? For getBeta setting type="Illumina" sets offset=100 as per Genome Studio. For getM setting type="" computes M-values as the logarithm of Meth/Unmeth, otherwise it is computed as the logit of getBeta(object).
offset	Offset in the beta ratio, see detail.
betaThreshold	Constrains the beta values to be in the inverval betwen betaThreshold and 1-betaThreshold.
dropRS	Should SNP probes be dropped?
dropCH	Should CH probes be dropped
...	For the constructor, additional arguments to be passed to SummarizedExperiment; of particular interest are colData, rowData and metadata. For getM these values gets passed onto getBeta.

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 = \frac{\textrm{Meth}}{\textrm{Meth} + \textrm{Unmeth} + \textrm{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 = \textrm{logit}(\beta) = \log(\textrm{Meth} / \textrm{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.

Value

An object of class MethylSet for the constructor.

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).

combine:

Combines two different MethylSet, eventually using the combine method for eSet.

Author(s)

Kasper Daniel Hansen [e-mail]

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")

kasperdanielhansen/minfi documentation built on Jan. 13, 2024, 9:30 p.m.