GenomicMethylSet-class: GenomicMethylSet instances

In kasperdanielhansen/minfi: Analyze Illumina Infinium DNA methylation arrays

GenomicMethylSet instances

Description

This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic location.

Usage

## Constructor

GenomicMethylSet(gr = GRanges(), Meth = new("matrix"),
                 Unmeth = new("matrix"), annotation = "",
                 preprocessMethod = "", ...)

## Data extraction / Accessors

## S4 method for signature 'GenomicMethylSet'
getMeth(object)
## S4 method for signature 'GenomicMethylSet'
getUnmeth(object)
## S4 method for signature 'GenomicMethylSet'
getBeta(object, type = "", offset = 0, betaThreshold = 0)
## S4 method for signature 'GenomicMethylSet'
getM(object, type = "", ...)
## S4 method for signature 'GenomicMethylSet'
getCN(object, ...)
## S4 method for signature 'GenomicMethylSet'
pData(object)
## S4 method for signature 'GenomicMethylSet'
sampleNames(object)
## S4 method for signature 'GenomicMethylSet'
featureNames(object)
## S4 method for signature 'GenomicMethylSet'
annotation(object)
## S4 method for signature 'GenomicMethylSet'
preprocessMethod(object)
## S4 method for signature 'GenomicMethylSet'
mapToGenome(object, ...)

Arguments

object	A GenomicMethylSet.
gr	A GRanges object.
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 character string.
preprocessMethod	A preprocess method character string.
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.
...	For the constructor, additional arguments to be passed to SummarizedExperiment; of particular interest are colData and metadata. For getM these values gets passed onto getBeta. For mapToGenome, this is ignored.

Details

For a detailed discussion of getBeta and getM see the deatils section of MethylSet.

Value

An object of class GenomicMethylSet for the constructor.

Constructor

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

Accessors

A number of useful accessors are inherited from RangedSummarizedExperiment.

In the following code, object is a GenomicMethylSet.

getMeth(object), getUnmeth(object)

Get the Meth or 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.

sampleNames(object), featureNames(object)

Get the sampleNames (colnames) or the featureNames (rownames).

preprocessMethod(object), annotation(object)

Get the preprocess method or annotation character.

Utilities

mapToGenome(object)

Since object is already mapped to the genome, this method simply returns object unchanged.

combine:

Combines two different GenomicMethylSet, eventually using the cbind method for SummarizedExperiment.

Author(s)

Kasper Daniel Hansen [e-mail]

See Also

RangedSummarizedExperiment in the SummarizedExperiment package for the basic class structure. Objects of this class are typically created by using the function mapToGenome on a MethylSet.

Examples

  showClass("GenomicMethylSet")

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