MethylationSet: MethylationSet instances

Description

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

Usage

methylationSet(betas, phenotypes, annotationDataFrame, annoString = "custom")
"betas"(object)
"getMs"(object, threshold = 1e-04)
"checkProbes"(object)
"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.

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.

Details

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

Examples

Run this code

showClass("MethylationSet")

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