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An \"intelligent\" import function,\nmethylumiR can read the Illumina text files and create a\nMethyLumiSet. methylumIDAT can directly read raw IDAT files\nfrom HumanMethylation27 and HumanMethylation450 microarrays.\nNormalization, background correction, and quality control\nfeatures for GoldenGate, Infinium, and Infinium HD arrays are\nalso included.", "Collate": "AllGenerics.R MethyLumiSet-class.R MethyLumiM-class.R\nMoreGenerics.R Methods.R bgcorr.R coercions.R data.R\ndetectionpval.R featureFilter.R mclapply_replace.R\nmethylData-class.R methylumIDAT.R methylumiCSV.R methylumiR.R\nnormalization.R plotNegOob.R qc.probe.plot.R readIDAT2.R\nstripMethyLumiSet.R utilities.R varFilter.R", "VignetteBuilder": "quarto", "URL": "https://seandavi.github.io/methylumi/,\nhttps://github.com/seandavi/methylumi", "BugReports": "https://github.com/seandavi/methylumi/issues", "License": "GPL-2", "Encoding": "UTF-8", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-08-14 16:33:14 UTC", "RemoteUrl": "https://github.com/bioc/methylumi", "RemoteRef": "HEAD", "RemoteSha": "4232eaf043694b8b8e2bfe1095f03185be39a8af", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-01 13:00:32 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "methylumi_2.59.3.tar.gz", "_fileid": "https://r2.ropensci.org/860b50952eb94affbd45e6fbee8ae779c111fd6ad5ab344a861510936dbff015", "_filesize": 6745391, "_sha256": "860b50952eb94affbd45e6fbee8ae779c111fd6ad5ab344a861510936dbff015", "_expires": "2027-02-09T14:19:14.000Z", "_created": "2026-11-01T13:00:32.000Z", "_published": "2026-11-01T14:19:16.806Z", "_upstream": "https://github.com/bioc/methylumi", "_status": "success", "_maintainer": { "name": "Sean Davis", "email": "seandavi@gmail.com", "login": "seandavi", "description": "Software developer, Pediatric oncologist, Cancer researcher, Data scientist and engineer, Community organizer", "uuid": 92435 }, "_jobs": [ { "job": 124856063347, "time": 426, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13085072592" }, { "job": 124856063326, "time": 746, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13085123364" }, { "job": 124856063532, "time": 738, "config": "linux-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13085008616" }, { "job": 124856063450, "time": 510, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "13086413074" }, { "job": 124856063349, "time": 483, "config": "macos-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13085713160" }, { "job": 124853435263, "time": 689, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13084103104" }, { "job": 124856063374, "time": 354, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13085042473" }, { "job": 124856063353, "time": 550, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13084724358" }, { "job": 124856063471, "time": 690, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13084489130" }, { "job": 124856063327, "time": 628, "config": "windows-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13085182617" } ], "_bioccheck": { "error": 2, "warning": 5, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41308361725", "_commit": { "id": "4232eaf043694b8b8e2bfe1095f03185be39a8af", "author": "Sean Davis ", "committer": "GitHub ", "message": "Install methylumi into the real library before building the pkgdown site (#52)\n\npkgdown::build_site(install = TRUE) installs the package into a temporary\nlibrary that exists only on the calling R process's .libPaths(). 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"MethyLumiQC-class", "negctls,MethyLumiQC,character-method", "negctls,MethyLumiQC,missing-method", "negctls.stderr,MethyLumiQC,character-method", "negctls.stderr,MethyLumiQC,missing-method", "negnorm,MethyLumiQC,character-method", "negnorm,MethyLumiQC,missing-method", "normctls,MethyLumiQC-method", "QCdata<-,MethyLumiSet,MethyLumiQC-method", "qcplot,MethyLumiQC-method", "unmethylated,MethyLumiQC-method" ] }, { "page": "methylumiR", "title": "Load data from an Illumina methylation platform", "topics": [ "methylumiR" ] }, { "page": "MethyLumiSet-class", "title": "Class '\"MethyLumiSet\"' for containing Illumina methylation data", "topics": [ "betas,MethyLumiSet-method", "betas<-,MethyLumiSet,matrix-method", "boxplot,MethyLumiSet-method", "combine,MethyLumiSet,MethyLumiSet-method", "combine27k450k,MethyLumiSet,MethyLumiSet-method", "controlData,MethyLumiSet-method", "controlData<-,MethyLumiSet", "controlTypes,MethyLumiSet-method", "corplot,MethyLumiSet-method", 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