MethylationSet instances

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Description

Container with the data needed to perform methylation analysis. MethylationSet inherits from eSet and contains meth matrix as assay data member.

Usage

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methylationSet(betas, phenotypes, annotationDataFrame, annoString = "custom")

## S4 method for signature 'MethylationSet'
betas(object)

## S4 method for signature 'MethylationSet'
getMs(object, threshold = 1e-04)

## S4 method for signature 'MethylationSet'
checkProbes(object)

## S4 method for signature 'MethylationSet'
checkSamples(object)

Arguments

betas

Matrix of beta values

phenotypes

Data.frame or AnnotatedDataFrame with the phenotypes

annotationDataFrame

Data.frame or AnnotatedDataFrame with the phenotypes with the annotation of the methylation sites. A column with the chromosomes named chr and a column with the positions names pos are required.

annoString

Character with the name of the annotation used.

object

MethylationSet

threshold

Numeric with the threshold to avoid 0s and 1s.

Details

FeatureData, which contains annotation data, is required to perform any of the analysis.

Value

MethylationSet

Methods (by generic)

  • betas: Get beta matrix

  • getMs: Get Ms values

  • checkProbes: Filter probes with annotation

  • checkSamples: Modify a MethylationSet to only contain common samples

Slots

assayData

Contains matrices with equal dimensions, and with column number equal to nrow(phenoData). assayData must contain a matrix meth with rows representing features (e.g., methylation probes sets) and columns representing samples.

phenoData

See eSet

annotation

See eSet

featureData

See eSet. fData should contain at least chromosome and positions columns.

Examples

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showClass("MethylationSet")