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.

AuthorSean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla
Date of publicationNone
MaintainerSean Davis <sdavis2@mail.nih.gov>
LicenseGPL-2
Version2.20.0

View on Bioconductor

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

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

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