methylumi: Handle Illumina methylation data

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("methylumi")
AuthorSean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla
Bioconductor views CpGIsland DNAMethylation Preprocessing QualityControl TwoChannel
Date of publicationNone
MaintainerSean Davis <sdavis2@mail.nih.gov>
LicenseGPL-2
Version2.20.0

View on Bioconductor

Functions

betas Man page
betas<- Man page
betas,GenomicMethylSet-method Man page
betas,MethylSet-method Man page
betas,MethyLumiM-method Man page
betas<-,MethyLumiSet,matrix-method Man page
betas,MethyLumiSet-method Man page
betas,RangedSummarizedExperiment-method Man page
boxplot,MethyLumiSet-method Man page
combine27k450k Man page
combine27k450k,MethyLumiSet,MethyLumiSet-method Man page
combine,MethyLumiM,MethyLumiM-method Man page
combine,MethyLumiQC,MethyLumiQC-method Man page
combine,MethyLumiSet,MethyLumiSet-method Man page
controlData Man page
controlData<- Man page
controlData<-,MethyLumiM,ANY-method Man page
controlData,MethyLumiM-method Man page
controlData<-,MethyLumiSet Man page
controlData,MethyLumiSet-method Man page
controlData<-,MethyLumiSet,MethyLumiQC-method Man page
controlTypes Man page
controlTypes,MethyLumiM-method Man page
controlTypes,MethyLumiQC-method Man page
controlTypes,MethyLumiSet-method Man page
corplot Man page
corplot,MethyLumiSet-method Man page
CpGs Man page
cy3 Man page
Cy3<- Man page
Cy3<-,MethyLumiQC,matrix-method Man page
Cy3.N Man page
Cy3.N,MethyLumiQC-method Man page
Cy3.N,MethyLumiSet-method Man page
cy5 Man page
Cy5<- Man page
Cy5<-,MethyLumiQC,matrix-method Man page
Cy5.N Man page
Cy5.N,MethyLumiQC-method Man page
Cy5.N,MethyLumiSet-method Man page
dataType Man page
dataType<- Man page
dataType<-,MethyLumiM,ANY-method Man page
dataType<-,MethyLumiM-method Man page
dataType,MethyLumiM-method Man page
designIItoMandU Man page
designItoMandU Man page
detection Man page
detection<- Man page
detection<-,MethyLumiM-method Man page
detection,MethyLumiM-method Man page
diagnostics Man page
diagnostics,methylData-method Man page
estimateM Man page
exprs,MethyLumiSet-method Man page
extractBarcodeAndPosition Man page
featureFilter Man page
featureFilter,MethyLumiM-method Man page
featureFilter,MethyLumiSet-method Man page
getAssayDataNameSubstitutions Man page
getBarcodes Man page
getHistory Man page
getHistory,MethyLumiM-method Man page
getHistory,MethyLumiSet-method Man page
getProtocolData Man page
hist,MethyLumiQC-method Man page
hist,MethyLumiSet-method Man page
IDATsToDFs Man page
IDATtoDF Man page
intensitiesByChannel Man page
intensitiesByChannel,MethyLumiM-method Man page
intensitiesByChannel,MethyLumiQC-method Man page
intensitiesByChannel,MethyLumiSet-method Man page
intensities.IB Man page
intensities.IB,MethyLumiSet,character-method Man page
intensities.IB,MethyLumiSet,missing-method Man page
intensities.M Man page
intensities.M,MethyLumiSet,character-method Man page
intensities.M,MethyLumiSet,missing-method Man page
intensities.OOB Man page
intensities.OOB.allelic Man page
intensities.OOB.allelic,MethyLumiSet,character,character-method Man page
intensities.OOB.allelic,MethyLumiSet,missing,missing-method Man page
intensities.OOB,MethyLumiSet,character-method Man page
intensities.OOB,MethyLumiSet,missing-method Man page
intensities.U Man page
intensities.U,MethyLumiSet,character-method Man page
intensities.U,MethyLumiSet,missing-method Man page
lumiCSV Man page
lumIDAT Man page
mergeProbeDesigns Man page
methylated Man page
methylated<- Man page
methylated,MethylSet-method Man page
methylated<-,MethyLumiM,ANY-method Man page
methylated<-,MethyLumi,matrix-method Man page
methylated,MethyLumi-method Man page
methylated,MethyLumiM-method Man page
methylated,MethyLumiQC-method Man page
methylated<-,MethyLumiSet,matrix-method Man page
methylated,MethyLumiSet-method Man page
methylated.N Man page
methylated.N<- Man page
methylated.N<-,methylData,matrix-method Man page
methylated.N,methylData-method Man page
methylated.N<-,MethyLumiM,ANY-method Man page
methylated.N,MethyLumiM-method Man page
methylData-class Man page
methylumi Man page
methylumi.bgcorr Man page
MethyLumi-class Man page
methylumiCSV Man page
methylumIDAT Man page
methylumi.diagnostics Man page
MethyLumiM Man page
[,MethyLumiM,ANY-method Man page
MethyLumiM-class Man page
methylumi-package Man page
MethyLumiQC-class Man page
methylumiR Man page
[,MethyLumiSet,ANY-method Man page
MethyLumiSet-class Man page
mldat Man page
NChannelSetToMethyLumiSet Man page
negctls Man page
negctls,MethyLumiM,character-method Man page
negctls,MethyLumiM,missing-method Man page
negctls,MethyLumiQC,character-method Man page
negctls,MethyLumiQC,missing-method Man page
negctls,MethyLumiSet,character-method Man page
negctls,MethyLumiSet,missing-method Man page
negctls.stderr Man page
negctls.stderr,MethyLumiQC,character-method Man page
negctls.stderr,MethyLumiQC,missing-method Man page
negctls.stderr,MethyLumiSet,character-method Man page
negctls.stderr,MethyLumiSet,missing-method Man page
negnorm Man page
negnorm,MethyLumiM,character-method Man page
negnorm,MethyLumiM,missing-method Man page
negnorm,MethyLumiQC,character-method Man page
negnorm,MethyLumiQC,missing-method Man page
negnorm,MethyLumiSet,character-method Man page
negnorm,MethyLumiSet,missing-method Man page
normalizeMethyLumiSet Man page
normctls Man page
normctls,MethyLumiM-method Man page
normctls,MethyLumiQC-method Man page
normctls,MethyLumiSet-method Man page
pairs,MethyLumiSet-method Man page
plotNAs Man page
plotNAs,methylData-method Man page
plotNegOob Man page
plotSampleIntensities Man page
plotSampleIntensities,MethyLumiSet-method Man page
probeNAs Man page
probeNAs,MethyLumiM-method Man page
probeNAs,MethyLumiSet-method Man page
psummary Man page
pval.detect Man page
pval.detect<- Man page
pval.detect,methylData-method Man page
pval.detect<-,methylData,numeric-method Man page
pvals Man page
pvals<- Man page
pvals<-,MethyLumi,matrix-method Man page
pvals,MethyLumi-method Man page
pvals,MethyLumiM-method Man page
QCdata Man page
QCdata<- Man page
QCdata,MethyLumiM-method Man page
QCdata<-,MethyLumiSet Man page
QCdata,MethyLumiSet-method Man page
QCdata<-,MethyLumiSet,MethyLumiQC-method Man page
qcplot Man page
qcplot,Methylumi-method Man page
qcplot,MethyLumiQC-method Man page
qcplot,MethyLumiSet-method Man page
qc.probe.plot Man page
sampleNAs Man page
sampleNAs,MethyLumiM-method Man page
sampleNAs,MethyLumiSet-method Man page
show,MethyLumiSet-method Man page
stripBeadNs Man page
stripBeadSDs Man page
stripMethyLumiSet Man page
stripOOB Man page
summary,MethyLumi-method Man page
total.intensity Man page
total.intensity,MethyLumiM-method Man page
total.intensity,MethyLumiSet-method Man page
unmethylated Man page
unmethylated<- Man page
unmethylated,MethylSet-method Man page
unmethylated<-,MethyLumiM,ANY-method Man page
unmethylated<-,MethyLumi,matrix-method Man page
unmethylated,MethyLumi-method Man page
unmethylated,MethyLumiM-method Man page
unmethylated,MethyLumiQC-method Man page
unmethylated<-,MethyLumiSet,matrix-method Man page
unmethylated,MethyLumiSet-method Man page
unmethylated.N Man page
unmethylated.N<- Man page
unmethylated.N<-,methylData,matrix-method Man page
unmethylated.N,methylData-method Man page
unmethylated.N<-,MethyLumiM,ANY-method Man page
unmethylated.N,MethyLumiM-method Man page
varFilter Man page
varFilter,MethyLumiM-method Man page
varFilter,MethyLumiSet-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllGenerics.R R/Methods.R R/MethyLumiM-class.R R/MethyLumiSet-class.R R/MoreGenerics.R R/bgcorr.R R/coercions.R R/detectionpval.R R/featureFilter.R R/mclapply_replace.R R/methylData-class.R R/methylumIDAT.R R/methylumiCSV.R R/methylumiR.R R/normalization.R R/plotNegOob.R R/qc.probe.plot.R R/readIDAT2.R R/stripMethyLumiSet.R R/utilities.R R/varFilter.R
README
build
build/vignette.rds
data
data/5318317007_A_Grn.idat
data/5318317007_A_Red.idat
data/5318317007_B_Grn.idat
data/5318317007_B_Red.idat
data/5318317007_C_Grn.idat
data/5318317007_C_Red.idat
data/CpGs.rda
data/datalist
data/mldat.rda
data/test27k.R
inst
inst/NEWS.methylumIDAT
inst/doc
inst/doc/methylumi.R
inst/doc/methylumi.Rnw
inst/doc/methylumi.pdf
inst/doc/methylumi450k.R
inst/doc/methylumi450k.Rnw
inst/doc/methylumi450k.pdf
inst/extdata
inst/extdata/exampledata.controls.txt
inst/extdata/exampledata.samples.txt
inst/extdata/samples.txt
inst/extdata/substitutions.txt
man
man/CpGs.Rd man/MethyLumi-class.Rd man/MethyLumiM-class.Rd man/MethyLumiQC-class.Rd man/MethyLumiSet-class.Rd man/estimateM.Rd man/extractBarcodeAndPosition.Rd man/featureFilter.Rd man/generics.Rd man/getAssayDataNameSubstitutions.Rd man/methylData-class.Rd man/methylumIDAT.Rd man/methylumi-package.Rd man/methylumiGenerics.Rd man/methylumiR.Rd man/mldat.Rd man/normalizeMethyLumiSet.Rd man/plotSampleIntensities.Rd man/qcplot.Rd man/stripBeadExtras.Rd man/varFilter.Rd
vignettes
vignettes/methylumi.Rnw
vignettes/methylumi450k.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.