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.

Author
Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla
Date of publication
None
Maintainer
Sean Davis <sdavis2@mail.nih.gov>
License
GPL-2
Version
2.20.0

View on Bioconductor

Man pages

CpGs
Data frame describing loci on the 27 and 450k arrays.
estimateM
Estimate methylation M-value matrix
extractBarcodeAndPosition
Extract the Barcode and Position Information from Sentrix ID
featureFilter
Annotation-based Filtering of Features (CpG sites) in a...
generics
methylumi accessors
getAssayDataNameSubstitutions
Return a data.frame of AssayData name substitutions.
methylData-class
Class '"methylData"', superclass for MethyLumiSet and...
MethyLumi-class
The base class for storing Illumina Methylation data
methylumIDAT
methylumIDAT
methylumiGenerics
Generics defined in methylumi
MethyLumiM-class
Class "MethyLumiM": for Illumina Methylation microarray data...
methylumi-package
Handle Illumina methylation data
MethyLumiQC-class
Class '"MethyLumiQC"' for holding Illumina methylation QC...
methylumiR
Load data from Illumina methylation platform
MethyLumiSet-class
Class '"MethyLumiSet"' for containing Illumina methylation...
mldat
Example SAM format Illumina methylation dataset
normalizeMethyLumiSet
Normalize a MethyLumiSet, accounting for dye bias
plotSampleIntensities
Plot the sample intensities.
qcplot
Methods for dealing with control data for Illumina...
stripBeadExtras
Strip excessive probe-level data from MethyLumiSets
varFilter
Variation-based Filtering of Features (CpG sites) in a...

Files in this package

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