Package index

Package overview

methylumi-package methylumi

Handle Illumina methylation data

Import

Reading Illumina data into a MethyLumiSet: final report text files, raw IDATs, and the lower-level IDAT readers.

methylumiR()

Load data from an Illumina methylation platform

methylumIDAT()

methylumIDAT

IDATsToMatrices()

convert multiple idats to matrices

IDATtoMatrix()

process a single IDAT (just the mean intensities)

extractBarcodeAndPosition()

Extract the barcode and position information from a Sentrix ID

Classes

The eSet-derived containers for methylation data and its controls.

MethyLumi-class methylated<-,MethyLumi,matrix-method methylated,MethyLumi-method unmethylated<-,MethyLumi,matrix-method unmethylated,MethyLumi-method pvals<-,MethyLumi,matrix-method pvals,MethyLumi-method summary,MethyLumi-method qcplot,Methylumi-method

The base class for storing Illumina Methylation data

methylData-class diagnostics,methylData-method methylated.N,methylData-method methylated.N<-,methylData,matrix-method plotNAs,methylData-method pval.detect,methylData-method pval.detect<-,methylData,numeric-method unmethylated.N,methylData-method unmethylated.N<-,methylData,matrix-method

Class "methylData", superclass for MethyLumiSet and MethyLumiM

MethyLumiSet-class Cy3.N,MethyLumiSet-method Cy5.N,MethyLumiSet-method QCdata,MethyLumiSet-method QCdata<-,MethyLumiSet [,MethyLumiSet,ANY-method betas,MethyLumiSet-method betas<-,MethyLumiSet,matrix-method boxplot,MethyLumiSet-method combine27k450k,MethyLumiSet,MethyLumiSet-method combine,MethyLumiSet,MethyLumiSet-method controlData,MethyLumiSet-method controlData<-,MethyLumiSet controlTypes,MethyLumiSet-method corplot,MethyLumiSet-method exprs,MethyLumiSet-method getHistory,MethyLumiSet-method hist,MethyLumiSet-method intensities.IB,MethyLumiSet,character-method intensities.IB,MethyLumiSet,missing-method intensities.M,MethyLumiSet,character-method intensities.M,MethyLumiSet,missing-method intensities.OOB.allelic,MethyLumiSet,character,character-method intensities.OOB.allelic,MethyLumiSet,missing,missing-method intensities.OOB,MethyLumiSet,character-method intensities.OOB,MethyLumiSet,missing-method intensities.U,MethyLumiSet,character-method intensities.U,MethyLumiSet,missing-method intensitiesByChannel,MethyLumiSet-method methylated,MethyLumiSet-method methylated<-,MethyLumiSet,matrix-method negctls.stderr,MethyLumiSet,character-method negctls.stderr,MethyLumiSet,missing-method negctls,MethyLumiSet,character-method negctls,MethyLumiSet,missing-method negnorm,MethyLumiSet,character-method negnorm,MethyLumiSet,missing-method normctls,MethyLumiSet-method pairs,MethyLumiSet-method plotSampleIntensities,MethyLumiSet-method probeNAs,MethyLumiSet-method qcplot,MethyLumiSet-method sampleNAs,MethyLumiSet-method show,MethyLumiSet-method total.intensity,MethyLumiSet-method unmethylated,MethyLumiSet-method unmethylated<-,MethyLumiSet,matrix-method [,MethyLumiSet,ANY,ANY,ANY-method

Class "MethyLumiSet" for containing Illumina methylation data

MethyLumiM-class MethyLumiM QCdata,MethyLumiM-method [,MethyLumiM,ANY-method betas,MethyLumiM-method combine,MethyLumiM,MethyLumiM-method controlData,MethyLumiM-method controlData<-,MethyLumiM,ANY-method controlTypes,MethyLumiM-method detection,MethyLumiM-method detection<-,MethyLumiM-method getHistory,MethyLumiM-method intensitiesByChannel,MethyLumiM-method methylated.N,MethyLumiM-method methylated.N<-,MethyLumiM,ANY-method methylated,MethyLumiM-method methylated<-,MethyLumiM,ANY-method negctls,MethyLumiM,character-method negctls,MethyLumiM,missing-method negnorm,MethyLumiM,character-method negnorm,MethyLumiM,missing-method normctls,MethyLumiM-method probeNAs,MethyLumiM-method pvals,MethyLumiM-method sampleNAs,MethyLumiM-method total.intensity,MethyLumiM-method unmethylated.N,MethyLumiM-method unmethylated.N<-,MethyLumiM,ANY-method unmethylated,MethyLumiM-method unmethylated<-,MethyLumiM,ANY-method dataType,MethyLumiM-method dataType<-,MethyLumiM,ANY-method dataType<-,MethyLumiM-method [,MethyLumiM,ANY,ANY,ANY-method

Class "MethyLumiM": for Illumina Methylation microarray data using logRatios

MethyLumiQC-class Cy3.N,MethyLumiQC-method Cy3<-,MethyLumiQC,matrix-method Cy5.N,MethyLumiQC-method Cy5<-,MethyLumiQC,matrix-method QCdata<-,MethyLumiSet,MethyLumiQC-method combine,MethyLumiQC,MethyLumiQC-method controlData<-,MethyLumiSet,MethyLumiQC-method controlTypes,MethyLumiQC-method hist,MethyLumiQC-method intensitiesByChannel,MethyLumiQC-method methylated,MethyLumiQC-method negctls.stderr,MethyLumiQC,character-method negctls.stderr,MethyLumiQC,missing-method negctls,MethyLumiQC,character-method negctls,MethyLumiQC,missing-method negnorm,MethyLumiQC,character-method negnorm,MethyLumiQC,missing-method normctls,MethyLumiQC-method qcplot,MethyLumiQC-method unmethylated,MethyLumiQC-method

Class "MethyLumiQC" for holding Illumina methylation QC data

Accessors and generics

Assay-data accessors (betas, methylated, unmethylated, pvals, QCdata) and the generics the classes above implement, including the coercions between MethyLumiSet, MethyLumiM and the minfi classes.

betas() pvals() methylated() unmethylated() getHistory() QCdata()

methylumi accessors

combine27k450k controlData controlData<- cy3 Cy3.N Cy3<- cy5 Cy5.N Cy5<- designIItoMandU designItoMandU detection detection<- diagnostics getBarcodes getProtocolData IDATsToDFs IDATtoDF intensities.IB intensities.M intensities.OOB intensities.OOB.allelic intensities.U intensitiesByChannel lumiCSV lumIDAT mergeProbeDesigns methylated.N methylated.N<- methylumi.bgcorr methylumi.diagnostics methylumiCSV NChannelSetToMethyLumiSet negctls negctls.stderr negnorm normctls plotNAs plotNegOob probeNAs psummary pval.detect pval.detect<- qc.probe.plot sampleNAs total.intensity unmethylated.N unmethylated.N<- dataType dataType<- betas,RangedSummarizedExperiment-method methylated,MethylSet-method unmethylated,MethylSet-method betas,GenomicMethylSet-method betas,MethylSet-method

Generics defined in methylumi

getAssayDataNameSubstitutions()

Return a data.frame of AssayData name substitutions

Preprocessing and normalization

Background correction, dye-bias and control normalization, M-value estimation, and the strippers that drop out-of-band and bead-level assays.

normalizeMethyLumiSet()

Normalize a MethyLumiSet, accounting for dye bias

estimateM()

Estimate methylation M-value matrix

stripBeadNs() stripBeadSDs() stripOOB() stripMethyLumiSet()

Strip excessive probe-level data from MethyLumiSets

Filtering

featureFilter()

Annotation-based filtering of features (CpG sites) in a MethyLumiSet or MethyLumiM object

varFilter()

Variation-based filtering of features (CpG sites) in a MethyLumiSet or MethyLumiM object

QC and plotting

qcplot() controlTypes()

Methods for dealing with control data for Illumina methylation data

plotSampleIntensities()

Plot the sample intensities

Pipelines

tcgaPipeline()

Total convenience function for processing IDATs like tcga

Example data

mldat

Example SAM format Illumina methylation dataset

CpGs

Data frame describing loci on the 27 and 450k arrays