minfi (version 1.18.2)

GenomicMethylSet-class: 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"), pData = DataFrame(),
                 annotation = "", preprocessMethod = "")
## Data extraction / Accessors
## S3 method for class 'GenomicMethylSet':
getMeth(object)
## S3 method for class 'GenomicMethylSet':
getUnmeth(object)
## S3 method for class 'GenomicMethylSet':
getBeta(object, type = "", offset = 0, betaThreshold = 0)
## S3 method for class 'GenomicMethylSet':
getM(object, type = "", \dots)
## S3 method for class 'GenomicMethylSet':
getCN(object, \dots)
## S3 method for class 'GenomicMethylSet':
pData(object)
## S3 method for class 'GenomicMethylSet':
sampleNames(object)
## S3 method for class 'GenomicMethylSet':
featureNames(object)
## S3 method for class 'GenomicMethylSet':
annotation(object)
## S3 method for class 'GenomicMethylSet':
preprocessMethod(object)
## S3 method for class 'GenomicMethylSet':
mapToGenome(object, \dots)

Arguments

object

A GenomicMethylSet.

gr

A GRanges object.

pData

A DataFrame or data.frame 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 getM these values gets passed onto getBeta. For mapToGenome, this is ignored.

Constructor

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

Details

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

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")