{
  "_id": "6a12a672acfb0bcc41d142c5",
  "Package": "wateRmelon",
  "Type": "Package",
  "Title": "Illumina DNA methylation array normalization and metrics",
  "Version": "2.19.0",
  "Authors@R": "c(person(c(\"Leo\", \"C\"), \"Schalkwyk\", role = c(\"cre\", \"aut\"),\nemail = \"lschal@essex.ac.uk\"),\nperson(c(\"Tyler\", \"J\"), \"Gorrie-Stone\", role = \"aut\"),\nperson(c(\"Ruth\"), \"Pidsley\", role = \"aut\"),\nperson(c(\"Chloe\", \"CY\"), \"Wong\", role = \"aut\"),\nperson(c(\"Nizar\"), \"Touleimat\", role='ctb'),\nperson(c(\"Matthieu\"), \"Defrance\", role='ctb'),\nperson(c(\"Andrew\"), \"Teschendorff\", role='ctb'),\nperson(c(\"Jovana\"), \"Maksimovic\", role='ctb'),\nperson(c(\"Louis\", \"Y\"), \"El Khoury\", role='ctb'),\nperson(c(\"Yucheng\"), \"Wang\", role='ctb'),\nperson(c(\"Alexandria\"), \"Andrayas\", role='ctb')\n)",
  "Description": "15 flavours of betas and three performance metrics, with\nmethods for objects produced by methylumi and minfi packages.",
  "License": "GPL-3",
  "LazyLoad": "yes",
  "biocViews": "DNAMethylation, Microarray, TwoChannel, Preprocessing,\nQualityControl",
  "Collate": "as.methylumi.R bscon.R bscon_methy.R bscon_minfi.R getAnn.R\noxyscale.R adaptRefQuantiles.R beta1.R Beta2M.R betaqn.R bgeq.R\nbgeqot.R bgeqq2.R bgeqqn.R BMIQ_1.1.R combo.R\ncreateAnnotation.R concatenateMatrices.R coRankedMatrices.R\ncorrectI.R correctII.R dataDetectPval2NA.R db1.R\ndetectionPval.filter.R dfs2.R dfsfit.R dmrse.R dmrse_col.R\ndmrse_row.R dyebuy1.R dyebuy2.R dyebuy3.R dyebuy4.R\nestimateCellCounts.R estimateSex.R filterXY.R\nfindAnnotationProbes.R gcoms.R gcose.R genki.R genkme.R\ngenkus.R genotype.R getMethylumiBeta.R getQuantiles.R\ngetSamples.R getsnp.R horv.R loadMethylumi2.R lumiMethyR2.R\nM2Beta.R melon.R nbBeadsFilter.R normalize.quantiles2.R\nnormalizeIlluminaMethylation.R ot.R outlyx.R pasteque.R\npeak.correction.R pfilter.R pipelineIlluminaMethylation.batch.R\npwod.R detection.R readEPIC.R preprocessIlluminaMethylation.R\nreferenceQuantiles.R adjustedDasen.R adjustedFunnorm.R\nrobustQuantileNorm_Illumina450K.probeCategories.R\nrobustQuantileNorm_Illumina450K.R seabird.R sextest.R summits.R\nswan2.R uniqueAnnotationCategory.R qual.R uSexQN.R smokp.R\nmanifesto.R readAny.R AllGenerics.R x_methylumi.R y_minfi.R\nz_bigmelon.R",
  "RoxygenNote": "7.3.1",
  "NeedsCompilation": "no",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "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": "2026-04-28 12:37:09 UTC",
  "RemoteUrl": "https://github.com/bioc/wateRmelon",
  "RemoteRef": "HEAD",
  "RemoteSha": "1bf46113dbb7c2611d26e15130d7b62917592167",
  "Packaged": {
    "Date": "2026-05-24 06:55:57 UTC",
    "User": "root"
  },
  "Author": "Leo C Schalkwyk [cre, aut],\nTyler J Gorrie-Stone [aut],\nRuth Pidsley [aut],\nChloe CY Wong [aut],\nNizar Touleimat [ctb],\nMatthieu Defrance [ctb],\nAndrew Teschendorff [ctb],\nJovana Maksimovic [ctb],\nLouis Y El Khoury [ctb],\nYucheng Wang [ctb],\nAlexandria Andrayas [ctb]",
  "Maintainer": "Leo C Schalkwyk <lschal@essex.ac.uk>",
  "MD5sum": "47bda6d58bd096eea76fdd475f75d784",
  "_user": "bioc",
  "_type": "src",
  "_file": "wateRmelon_2.19.0.tar.gz",
  "_fileid": "0363c58a18901e3b1777a98c9d048ec20eaeb43d3924f567bc69824aa7239e2e",
  "_filesize": 3524412,
  "_sha256": "0363c58a18901e3b1777a98c9d048ec20eaeb43d3924f567bc69824aa7239e2e",
  "_created": "2026-05-24T06:55:57.000Z",
  "_published": "2026-05-24T07:19:14.630Z",
  "_jobs": [
    {
      "job": 77578767185,
      "time": 610,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7183114954"
    },
    {
      "job": 77578767199,
      "time": 936,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7183154800"
    },
    {
      "job": 77578767198,
      "time": 887,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7183148287"
    },
    {
      "job": 77578767203,
      "time": 776,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7183197893"
    },
    {
      "job": 77578767202,
      "time": 461,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7183171131"
    },
    {
      "job": 77578096422,
      "time": 790,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7183048683"
    },
    {
      "job": 77578767187,
      "time": 578,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7183111319"
    },
    {
      "job": 77578767212,
      "time": 759,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7183131755"
    },
    {
      "job": 77578767229,
      "time": 666,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7183121292"
    },
    {
      "job": 77578767227,
      "time": 768,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7183132730"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 3,
    "note": 22
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26354300752",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/wateRmelon",
  "_commit": {
    "id": "1bf46113dbb7c2611d26e15130d7b62917592167",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379829
  },
  "_maintainer": {
    "name": "Leo C Schalkwyk",
    "email": "lschal@essex.ac.uk",
    "login": "schalkwyk",
    "description": "",
    "uuid": 22239004
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "limma",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "matrixStats",
      "role": "Depends"
    },
    {
      "package": "methylumi",
      "role": "Depends"
    },
    {
      "package": "lumi",
      "role": "Depends"
    },
    {
      "package": "ROC",
      "role": "Depends"
    },
    {
      "package": "IlluminaHumanMethylation450kanno.ilmn12.hg19",
      "role": "Depends"
    },
    {
      "package": "illuminaio",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "RPMM",
      "role": "Suggests"
    },
    {
      "package": "IlluminaHumanMethylationEPICanno.ilm10b2.hg19",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "IlluminaHumanMethylationEPICmanifest",
      "role": "Suggests"
    },
    {
      "package": "irlba",
      "role": "Suggests"
    },
    {
      "package": "FlowSorted.Blood.EPIC",
      "role": "Suggests"
    },
    {
      "package": "FlowSorted.Blood.450k",
      "role": "Suggests"
    },
    {
      "package": "preprocessCore",
      "role": "Suggests"
    },
    {
      "package": "minfi",
      "role": "Enhances"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 6,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.19.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.18.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "dnamethylation",
    "microarray",
    "twochannel",
    "preprocessing",
    "qualitycontrol"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 1475,
    "source": "https://www.bioconductor.org/packages/stats/bioc/wateRmelon"
  },
  "_mentions": 108,
  "_searchresults": 338,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/wateRmelon.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "adaptRefQuantiles",
    "adjustedDasen",
    "adjustedFunnorm",
    "agep",
    "anSNP",
    "anti.trafo",
    "aoget",
    "as.methylumi",
    "auc_probability",
    "beadc",
    "beadcount",
    "Beta2M",
    "betaqn",
    "bfp",
    "bgIntensitySwan.methylumi",
    "BMIQ",
    "bscon",
    "bscon_methy",
    "bscon_minfi",
    "canno",
    "CheckBMIQ",
    "colnames",
    "columnMatrix",
    "combo",
    "concatenateMatrices",
    "coRankedMatrices",
    "correctI",
    "correctII",
    "danen",
    "danes",
    "danet",
    "dasen",
    "dataDetectPval2NA",
    "DataToNChannelSet2",
    "daten1",
    "daten2",
    "db1",
    "designIItoMandU2",
    "designItoMandU2",
    "detectionPval.filter",
    "detectP",
    "dfort",
    "dfs2",
    "dfsfit",
    "dmrse",
    "dmrse_col",
    "dmrse_row",
    "epicv2clean",
    "epicv2clean.default",
    "epicv2clean.gds.class",
    "estimateCellCounts.wateRmelon",
    "estimateCellCounts.wmln",
    "estimateSex",
    "extractAssayDataFromList2",
    "filterXY",
    "findAnnotationProbes",
    "fot",
    "fuks",
    "gcoms",
    "gcose",
    "genall",
    "generateManifest",
    "genki",
    "genkme",
    "genkus",
    "genme",
    "genus",
    "getControlProbes2",
    "getMethylationBeadMappers2",
    "getMethylumiBeta",
    "getQuantiles",
    "getSamples",
    "getsnp",
    "goodSNP",
    "got",
    "IDATsToMatrices2",
    "IDATtoMatrix2",
    "idet",
    "iDMR",
    "iqrFun",
    "loadMethylumi2",
    "lumiMethyR2",
    "M2Beta",
    "mergeProbeDesigns2",
    "methylumIDATepic",
    "metrics",
    "mvFun",
    "nanes",
    "nanet",
    "nasen",
    "naten",
    "nbBeadsFilter",
    "NChannelSetToMethyLumiSet2",
    "normalize.quantiles2",
    "normalizeIlluminaMethylation",
    "outlyx",
    "oxyscale",
    "p_dfsfit",
    "pcouted",
    "pfilter",
    "pipelineIlluminaMethylation.batch",
    "plot_predicted_sex",
    "preprocessIlluminaMethylation",
    "pwod",
    "qual",
    "read.manifest",
    "readEPIC",
    "readPepo",
    "referenceQuantiles",
    "robustQuantileNorm_Illumina450K",
    "robustQuantileNorm_Illumina450K.probeCategories",
    "seabi",
    "seabi2",
    "seabird",
    "seabird2",
    "sextest",
    "smokp",
    "sort_order",
    "subbo",
    "summits",
    "swan",
    "tie_norm",
    "tost",
    "trafo",
    "uniqueAnnotationCategory",
    "uSexQN",
    "uSexQNengine"
  ],
  "_datasets": [
    {
      "name": "ageCoefs",
      "title": "",
      "object": "age_coefficients",
      "file": "age_coefficients.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "coef",
      "title": "Age Prediction from methylomic expression data",
      "object": "coef",
      "file": "coef.rda",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "epic.controls",
      "title": "readEPIC",
      "object": "epic.controls",
      "file": "epic.controls.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Address",
        "Type",
        "Color_Channel",
        "Name"
      ],
      "rows": 635,
      "table": true,
      "tojson": true
    },
    {
      "name": "epicV2.controls",
      "title": "",
      "object": "epicV2.controls",
      "file": "epicV2.controls.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Address",
        "Type",
        "Color_Channel",
        "Name"
      ],
      "rows": 635,
      "table": true,
      "tojson": true
    },
    {
      "name": "hannumCoef",
      "title": "Age Prediction from methylomic expression data",
      "object": "hannumCoef",
      "file": "hannumCoef.rda",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "iDMR",
      "title": "Imprinting differentially methylated region probes of Illumina 450 arrays",
      "object": "iDMR",
      "file": "iDMR.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "melon",
      "title": "Small MethyLumi data set for examples and testing",
      "object": "melon",
      "file": "melon.rda",
      "class": [
        "MethyLumiSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sex_coef",
      "title": "",
      "object": "sexCoef",
      "file": "sexCoef.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "IlmnID",
        "CHR",
        "pca",
        "mean",
        "coeff"
      ],
      "rows": 453152,
      "table": true,
      "tojson": true
    },
    {
      "name": "smokp_cpgs",
      "title": "Smoking Prediction from methylomic expression data",
      "object": "smokp_cpgs",
      "file": "smokp_cpgs.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "wateRmelon-package",
      "title": "Illumina 450K arrays: normalization and performance metrics",
      "topics": [
        "wateRmelon-package",
        "wateRmelon"
      ]
    },
    {
      "page": "dot-createAnnotation",
      "title": "Internal function to guess correct pData and retrieve using minfi",
      "topics": [
        ".createAnnotation"
      ]
    },
    {
      "page": "dot-getManifestString",
      "title": "Internal functions for Illumina i450 normalization functions",
      "topics": [
        ".getManifestString",
        "fot",
        "got",
        "pop"
      ]
    },
    {
      "page": "adaptRefQuantiles",
      "title": "Functions from 450-pipeline (Touleimat & Tost)",
      "topics": [
        "adaptRefQuantiles",
        "bgIntensitySwan.methylumi",
        "concatenateMatrices",
        "coRankedMatrices",
        "dataDetectPval2NA",
        "detectionPval.filter",
        "filterXY",
        "findAnnotationProbes",
        "getMethylumiBeta",
        "getQuantiles",
        "getSamples",
        "loadMethylumi2",
        "lumiMethyR2",
        "nbBeadsFilter",
        "normalize.quantiles2",
        "normalizeIlluminaMethylation",
        "pipelineIlluminaMethylation.batch",
        "preprocessIlluminaMethylation",
        "referenceQuantiles",
        "robustQuantileNorm_Illumina450K",
        "robustQuantileNorm_Illumina450K.probeCategories",
        "uniqueAnnotationCategory"
      ]
    },
    {
      "page": "adjustedDasen",
      "title": "adjustedDasen",
      "topics": [
        "adjustedDasen"
      ]
    },
    {
      "page": "adjustedFunnorm",
      "title": "adjustedFunnorm",
      "topics": [
        "adjustedFunnorm"
      ]
    },
    {
      "page": "agep",
      "title": "Age Prediction from methylomic expression data",
      "topics": [
        "agep",
        "agep,MethylSet-method",
        "agep,MethyLumiSet-method",
        "agep,RGChannelSet-method",
        "age_coefficients",
        "coef",
        "hannumCoef"
      ]
    },
    {
      "page": "as.methylumi-methods",
      "title": "Methods for Function 'as.methylumi'",
      "topics": [
        "as.methylumi",
        "as.methylumi,ANY-method",
        "as.methylumi,MethylSet-method",
        "as.methylumi,MethyLumiSet-method",
        "as.methylumi-methods",
        "getColumns"
      ]
    },
    {
      "page": "beadc",
      "title": "Calculates the number of samples with bead count <3 for each probe in matrix of bead count values",
      "topics": [
        "beadc"
      ]
    },
    {
      "page": "beadcount",
      "title": "Creates matrix of beacounts from minfi data.",
      "topics": [
        "beadcount"
      ]
    },
    {
      "page": "Beta2M",
      "title": "Internal functions for peak.correction (fuks)",
      "topics": [
        "Beta2M",
        "correctI",
        "correctII",
        "M2Beta",
        "summits"
      ]
    },
    {
      "page": "dasen-exprmethy450",
      "title": "Calculate normalized betas from exprmethy450 of Illumina 450K methylation arrays",
      "topics": [
        "betaqn,exprmethy450-method",
        "fuks,exprmethy450-method"
      ]
    },
    {
      "page": "BMIQ",
      "title": "Beta-Mixture Quantile (BMIQ) Normalisation method for Illumina 450k arrays",
      "topics": [
        "BMIQ",
        "BMIQ,ANY-method",
        "BMIQ,MethylSet-method",
        "BMIQ,MethyLumiSet-method",
        "BMIQ-methods",
        "CheckBMIQ"
      ]
    },
    {
      "page": "bscon",
      "title": "Calculate bisulphite conversion",
      "topics": [
        "bscon",
        "bscon,MethyLumiSet-method",
        "bscon,RGChannelSet-method"
      ]
    },
    {
      "page": "canno",
      "title": "canno - process csv manifest into annotation object for illumina methylation preprocessing",
      "topics": [
        "canno"
      ]
    },
    {
      "page": "colnames-methods",
      "title": "Methods for Function 'colnames' in Package 'wateRmelon'",
      "topics": [
        "colnames,MethyLumiSet-method",
        "colnames-methods"
      ]
    },
    {
      "page": "combo",
      "title": "Combine MethyLumiSet objects",
      "topics": [
        "combo"
      ]
    },
    {
      "page": "dasen",
      "title": "Calculate normalized betas from Illumina 450K methylation arrays",
      "topics": [
        "betaqn",
        "danen",
        "danes",
        "danet",
        "dasen",
        "daten1",
        "daten2",
        "fuks",
        "nanes",
        "nanet",
        "nasen",
        "naten",
        "swan",
        "tost"
      ]
    },
    {
      "page": "dasen-MethyLumiSet",
      "title": "Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays",
      "topics": [
        "betaqn,MethyLumiSet-method",
        "danen,MethyLumiSet-method",
        "danes,MethyLumiSet-method",
        "danet,MethyLumiSet-method",
        "dasen,MethyLumiSet-method",
        "daten1,MethyLumiSet-method",
        "daten2,MethyLumiSet-method",
        "fuks,MethyLumiSet-method",
        "nanes,MethyLumiSet-method",
        "nanet,MethyLumiSet-method",
        "nasen,MethyLumiSet-method",
        "naten,MethyLumiSet-method",
        "swan,MethyLumiSet-method",
        "tost,MethyLumiSet-method"
      ]
    },
    {
      "page": "dasen-MethySet",
      "title": "Calculate normalized betas from Illumina 450K methylation arrays",
      "topics": [
        "betaqn,MethylSet-method",
        "betaqn,RGChannelSet-method",
        "danen,MethylSet-method",
        "danen,RGChannelSet-method",
        "danes,MethylSet-method",
        "danes,RGChannelSet-method",
        "danet,MethylSet-method",
        "danet,RGChannelSet-method",
        "dasen,MethylSet-method",
        "dasen,RGChannelSet-method",
        "daten1,MethylSet-method",
        "daten1,RGChannelSet-method",
        "daten2,MethylSet-method",
        "daten2,RGChannelSet-method",
        "fuks,MethylSet-method",
        "fuks,RGChannelSet-method",
        "nanes,MethylSet-method",
        "nanes,RGChannelSet-method",
        "nanet,MethylSet-method",
        "nanet,RGChannelSet-method",
        "nasen,MethylSet-method",
        "nasen,RGChannelSet-method",
        "naten,MethylSet-method",
        "naten,RGChannelSet-method",
        "swan,MethylSet-method",
        "swan,RGChannelSet-method",
        "tost,MethylSet-method",
        "tost,RGChannelSet-method"
      ]
    },
    {
      "page": "db1",
      "title": "Internal wateRmelon functions for calculating betas",
      "topics": [
        "db1",
        "dfs2",
        "dfsfit"
      ]
    },
    {
      "page": "dmrse",
      "title": "Standard error of iDMR 450k array DNA methylation features",
      "topics": [
        "dmrse",
        "dmrse_col",
        "dmrse_row"
      ]
    },
    {
      "page": "dmrse-methods",
      "title": "Methods for Function 'dmrse' in Package 'wateRmelon'",
      "topics": [
        "dmrse,exprmethy450-method",
        "dmrse,MethylSet-method",
        "dmrse,MethyLumiSet-method",
        "dmrse,RGChannelSet-method",
        "dmrse-methods",
        "dmrse_col,exprmethy450-method",
        "dmrse_col,MethylSet-method",
        "dmrse_col,MethyLumiSet-method",
        "dmrse_col,RGChannelSet-method",
        "dmrse_col-methods",
        "dmrse_row,exprmethy450-method",
        "dmrse_row,MethylSet-method",
        "dmrse_row,MethyLumiSet-method",
        "dmrse_row,RGChannelSet-method",
        "dmrse_row-methods"
      ]
    },
    {
      "page": "epicv2clean.default",
      "title": "Strip and subset EPICv2 data to work with legacy data and methods",
      "topics": [
        "epicv2clean",
        "epicv2clean.default",
        "epicv2clean.gds.class"
      ]
    },
    {
      "page": "estimateCellCounts.wmln",
      "title": "Cell Proportion Estimation using wateRmelon",
      "topics": [
        "estimateCellCounts.wateRmelon",
        "estimateCellCounts.wateRmelon,MethylSet-method",
        "estimateCellCounts.wateRmelon,MethyLumiSet-method",
        "estimateCellCounts.wateRmelon,RGChannelSet-method",
        "estimateCellCounts.wmln"
      ]
    },
    {
      "page": "estimateSex",
      "title": "Predict sex by using robust sex-related CpG sites on ChrX and ChrY",
      "topics": [
        "estimateSex"
      ]
    },
    {
      "page": "genki",
      "title": "SNP derived performance metrics for Illumina 450K DNA methylation arrays.",
      "topics": [
        "genki"
      ]
    },
    {
      "page": "genki-methods",
      "title": "Methods for Function 'genki' in Package 'wateRmelon'",
      "topics": [
        "genki,exprmethy450-method",
        "genki,MethylSet-method",
        "genki,MethyLumiSet-method",
        "genki,RGChannelSet-method",
        "genki-methods"
      ]
    },
    {
      "page": "genkme",
      "title": "Internal functions for genotype-based normalization metrics",
      "topics": [
        "gcoms",
        "gcose",
        "genkme",
        "genkus",
        "getsnp"
      ]
    },
    {
      "page": "got",
      "title": "Internal functions for Illumina i450 normalization functions",
      "topics": [
        "fot",
        "got"
      ]
    },
    {
      "page": "idet",
      "title": "idet - identify idats by a hash of the addresses",
      "topics": [
        "idet"
      ]
    },
    {
      "page": "iDMR",
      "title": "Imprinting differentially methylated region probes of Illumina 450 arrays",
      "topics": [
        "iDMR"
      ]
    },
    {
      "page": "melon",
      "title": "Small MethyLumi data set for examples and testing",
      "topics": [
        "melon"
      ]
    },
    {
      "page": "metrics",
      "title": "Calculate a full set of 450K normalization/performance metrics",
      "topics": [
        "metrics"
      ]
    },
    {
      "page": "NChannelSetToMethyLumiSet2",
      "title": "For internal use, is read using minfi-like machinery and then preprocessed into the more flexible and convenient methylumi object used by wateRmelon/bigmelon",
      "topics": [
        "NChannelSetToMethyLumiSet2"
      ]
    },
    {
      "page": "outlyx",
      "title": "Identify Outliers within Methylumi and Minfi packaged objects",
      "topics": [
        "outlyx"
      ]
    },
    {
      "page": "outlyx-methods",
      "title": "Methods for Function 'outlyx' in Package 'wateRmelon'",
      "topics": [
        "outlyx,MethylSet-method",
        "outlyx,MethyLumiSet-method",
        "outlyx,RGChannelSet-method"
      ]
    },
    {
      "page": "pfilter",
      "title": "Basic data filtering for Illumina 450 methylation data",
      "topics": [
        "pfilter",
        "pfilter,MethyLumiSet-method",
        "pfilter,RGChannelSetExtended-method",
        "pfilter-methods"
      ]
    },
    {
      "page": "pwod",
      "title": "Probe-Wise Outlier Detection",
      "topics": [
        "pwod"
      ]
    },
    {
      "page": "pwod-methods",
      "title": "Methods for Function 'pwod' in Package 'wateRmelon'",
      "topics": [
        "pwod,MethylSet-method",
        "pwod,MethyLumiSet-method",
        "pwod,RGChannelSet-method"
      ]
    },
    {
      "page": "qual",
      "title": "A measure of Normalization Violence",
      "topics": [
        "qual"
      ]
    },
    {
      "page": "read.manifest",
      "title": "read.manifest - read in csv format Illumina chip manifest files",
      "topics": [
        "read.manifest"
      ]
    },
    {
      "page": "readEPIC",
      "title": "readEPIC",
      "topics": [
        "epic.controls",
        "readEPIC"
      ]
    },
    {
      "page": "readPepo",
      "title": "readPepo - read (any kind of) Illumina DNA methylation array idat files into a methylumi object",
      "topics": [
        "readPepo"
      ]
    },
    {
      "page": "seabi",
      "title": "Calculate a performance metric based on male-female differences for Illumina methylation 450K arrays",
      "topics": [
        "seabi"
      ]
    },
    {
      "page": "seabi-methods",
      "title": "Methods for Function 'seabi' in Package 'wateRmelon'",
      "topics": [
        "seabi,exprmethy450-method",
        "seabi,MethylSet-method",
        "seabi,MethyLumiSet-method",
        "seabi,RGChannelSet-method",
        "seabi-methods"
      ]
    },
    {
      "page": "seabird",
      "title": "Calculate ROC area-under-curve for X-chromosome sex differences (internal function for calculating the seabi metric)",
      "topics": [
        "seabird"
      ]
    },
    {
      "page": "sextest",
      "title": "Test Illumina methylation 450K array probes for sex difference (internal function for calculating 'seabi' performance metric)",
      "topics": [
        "sextest"
      ]
    },
    {
      "page": "smokp",
      "title": "Smoking Prediction from methylomic expression data",
      "topics": [
        "smokp",
        "smokp,MethylSet-method",
        "smokp,MethyLumiSet-method",
        "smokp,RGChannelSet-method",
        "smokp_cpgs"
      ]
    },
    {
      "page": "wm_internal",
      "title": "Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1",
      "topics": [
        "anSNP",
        "anti.trafo",
        "aoget",
        "auc_probability",
        "bfp",
        "bscon_methy",
        "bscon_minfi",
        "columnMatrix",
        "DataToNChannelSet2",
        "designIItoMandU2",
        "designItoMandU2",
        "dfort",
        "extractAssayDataFromList2",
        "genall",
        "generateManifest",
        "genme",
        "genus",
        "getControlProbes2",
        "getMethylationBeadMappers2",
        "goodSNP",
        "IDATsToMatrices2",
        "IDATtoMatrix2",
        "iqrFun",
        "mergeProbeDesigns2",
        "methylumIDATepic",
        "mvFun",
        "NChannelSetToMethyLumiSet2",
        "oxyscale",
        "pcouted",
        "plot_predicted_sex",
        "p_dfsfit",
        "seabi2",
        "seabird2",
        "sort_order",
        "subbo",
        "tie_norm",
        "trafo",
        "uSexQN",
        "uSexQN,MethylSet-method",
        "uSexQN,MethyLumiSet-method",
        "uSexQN,RGChannelSet-method",
        "uSexQNengine"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/wateRmelon/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "affy",
    "affyio",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "base64",
    "beanplot",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocManager",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bumphunter",
    "cachem",
    "cigarillo",
    "cli",
    "clipr",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "DelayedMatrixStats",
    "digest",
    "dir.expiry",
    "doRNG",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "FDb.InfiniumMethylation.hg19",
    "filelock",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "genefilter",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "GEOquery",
    "ggplot2",
    "glue",
    "gtable",
    "h5mread",
    "HDF5Array",
    "highr",
    "hms",
    "httr",
    "httr2",
    "IlluminaHumanMethylation450kanno.ilmn12.hg19",
    "illuminaio",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "lumi",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "mclust",
    "memoise",
    "methylumi",
    "mgcv",
    "mime",
    "minfi",
    "multtest",
    "nleqslv",
    "nlme",
    "nor1mix",
    "openssl",
    "org.Hs.eg.db",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "preprocessCore",
    "prettyunits",
    "progress",
    "purrr",
    "quadprog",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "readr",
    "rentrez",
    "reshape",
    "reshape2",
    "restfulr",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "Rhtslib",
    "rjson",
    "rlang",
    "rngtools",
    "ROC",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "scrime",
    "selectr",
    "Seqinfo",
    "siggenes",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "TxDb.Hsapiens.UCSC.hg19.knownGene",
    "tzdb",
    "UCSC.utils",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "wateRmelon.Rmd",
      "filename": "wateRmelon.html",
      "title": "The wateRmelon User's Guide",
      "author": "Tyler Gorrie-Stone, Leonard Schalkwyk",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Citing the wateRmelon R package",
        "Installation",
        "Quick Start",
        "Data Import",
        "Quality Control",
        "Outlier Detection",
        "Probe Filtering",
        "Phenotype Predition",
        "Epigenetic Ages",
        "Sex",
        "Cell-type proportions",
        "Normalization & Preprocessing",
        "Normalization Violence",
        "Performance Metrics",
        "Genomic Imprinting",
        "SNP Genotypes",
        "XCI",
        "Statistical Analysis",
        "Session info"
      ],
      "created": "2023-09-04 09:24:35",
      "modified": "2023-09-05 15:03:08",
      "commits": 3
    }
  ],
  "_score": 7.952981225695143,
  "_indexed": true,
  "_nocasepkg": "watermelon",
  "_universes": [
    "bioc",
    "schalkwyk"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.19.0",
      "date": "2026-05-24T07:07:12.000Z",
      "distro": "noble",
      "commit": "1bf46113dbb7c2611d26e15130d7b62917592167",
      "fileid": "6ab2c43631d116bcfd55080b10d424e9bcedd2cf13ad3e3772e770c01c2f7cfa",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26354300752"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.19.0",
      "date": "2026-05-24T07:06:54.000Z",
      "distro": "noble",
      "commit": "1bf46113dbb7c2611d26e15130d7b62917592167",
      "fileid": "55e96cf4a2367890cba1e47c972b3709608f012e8e4957d77a0bc0eff73877f3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26354300752"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.19.0",
      "date": "2026-05-24T07:13:08.000Z",
      "commit": "1bf46113dbb7c2611d26e15130d7b62917592167",
      "fileid": "3134d45c09e848ab929d5e2fe43596d0db693acf5726da22fb258be2ea102328",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26354300752"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.19.0",
      "date": "2026-05-24T07:11:32.000Z",
      "commit": "1bf46113dbb7c2611d26e15130d7b62917592167",
      "fileid": "9b67ff31fafaff268c25efd1d875a0c2149e56c93b7aa36faf4eba9d692e2225",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26354300752"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.19.0",
      "date": "2026-05-24T07:06:41.000Z",
      "commit": "1bf46113dbb7c2611d26e15130d7b62917592167",
      "fileid": "266287db79e3d0cbef808c062aae0b095f9f7f290fb69f1ab9daf408dbe9ee47",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26354300752"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.19.0",
      "date": "2026-05-24T07:03:19.000Z",
      "commit": "1bf46113dbb7c2611d26e15130d7b62917592167",
      "fileid": "f64271056fcb4521a13ec91e3e57d4be6035517b9b2406d26319649495a8e316",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26354300752"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.19.0",
      "date": "2026-05-24T07:02:42.000Z",
      "commit": "1bf46113dbb7c2611d26e15130d7b62917592167",
      "fileid": "65f08d4fefb538e0463b3ece31f614b7edc93041e157ded3fecb2f869aa238ca",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26354300752"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.19.0",
      "date": "2026-05-24T07:03:21.000Z",
      "commit": "1bf46113dbb7c2611d26e15130d7b62917592167",
      "fileid": "1ff054b6c43f8edae88c00dd82b85812ccdd9659e589c718b68b65d1d8b3b4c2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26354300752"
    }
  ]
}