Package: wateRmelon 2.19.0

Leo C Schalkwyk

wateRmelon: Illumina DNA methylation array normalization and metrics

15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.

Authors:Leo C Schalkwyk [cre, aut], Tyler J Gorrie-Stone [aut], Ruth Pidsley [aut], Chloe CY Wong [aut], Nizar Touleimat [ctb], Matthieu Defrance [ctb], Andrew Teschendorff [ctb], Jovana Maksimovic [ctb], Louis Y El Khoury [ctb], Yucheng Wang [ctb], Alexandria Andrayas [ctb]

wateRmelon_2.19.0.tar.gz
wateRmelon_2.19.0.zip(r-4.7)wateRmelon_2.19.0.zip(r-4.6)wateRmelon_2.19.0.zip(r-4.5)
wateRmelon_2.19.0.tgz(r-4.6-any)wateRmelon_2.19.0.tgz(r-4.5-any)
wateRmelon_2.19.0.tar.gz(r-4.7-any)wateRmelon_2.19.0.tar.gz(r-4.6-any)
wateRmelon_2.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
wateRmelon/json (API)

# Install 'wateRmelon' in R:
install.packages('wateRmelon', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • coef - Age Prediction from methylomic expression data
  • epic.controls - ReadEPIC
  • hannumCoef - Age Prediction from methylomic expression data
  • iDMR - Imprinting differentially methylated region probes of Illumina 450 arrays
  • melon - Small MethyLumi data set for examples and testing
  • smokp_cpgs - Smoking Prediction from methylomic expression data

On BioConductor:wateRmelon-2.19.0(bioc 3.24)wateRmelon-2.18.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dnamethylationmicroarraytwochannelpreprocessingqualitycontrol

7.95 score 6 packages 338 scripts 1.5k downloads 108 mentions 127 exports 164 dependencies

Last updated from:1bf46113db. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR610
linux-devel-x86_64WARNING936
source / vignettesOK790
linux-release-x86_64WARNING887
macos-release-arm64WARNING461
macos-oldrel-arm64WARNING776
windows-develWARNING759
windows-releaseWARNING768
windows-oldrelWARNING666
wasm-releaseOK578

Exports:adaptRefQuantilesadjustedDasenadjustedFunnormagepanSNPanti.trafoaogetas.methylumiauc_probabilitybeadcbeadcountBeta2MbetaqnbfpbgIntensitySwan.methylumiBMIQbsconbscon_methybscon_minficannoCheckBMIQcolnamescolumnMatrixcomboconcatenateMatricescoRankedMatricescorrectIcorrectIIdanendanesdanetdasendataDetectPval2NADataToNChannelSet2daten1daten2db1designIItoMandU2designItoMandU2detectionPval.filterdetectPdfortdfs2dfsfitdmrsedmrse_coldmrse_rowepicv2cleanepicv2clean.defaultepicv2clean.gds.classestimateCellCounts.wateRmelonestimateCellCounts.wmlnestimateSexextractAssayDataFromList2filterXYfindAnnotationProbesfotfuksgcomsgcosegenallgenerateManifestgenkigenkmegenkusgenmegenusgetControlProbes2getMethylationBeadMappers2getMethylumiBetagetQuantilesgetSamplesgetsnpgoodSNPgotIDATsToMatrices2IDATtoMatrix2idetiDMRiqrFunloadMethylumi2lumiMethyR2M2BetamergeProbeDesigns2methylumIDATepicmetricsmvFunnanesnanetnasennatennbBeadsFilterNChannelSetToMethyLumiSet2normalize.quantiles2normalizeIlluminaMethylationoutlyxoxyscalep_dfsfitpcoutedpfilterpipelineIlluminaMethylation.batchplot_predicted_sexpreprocessIlluminaMethylationpwodqualread.manifestreadEPICreadPeporeferenceQuantilesrobustQuantileNorm_Illumina450KrobustQuantileNorm_Illumina450K.probeCategoriesseabiseabi2seabirdseabird2sextestsmokpsort_ordersubbosummitsswantie_normtosttrafouniqueAnnotationCategoryuSexQNuSexQNengine

Dependencies:abindaffyaffyioannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemcigarilloclicliprcodetoolscpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdir.expirydoRNGdplyrevaluatefarverfastmapFDb.InfiniumMethylation.hg19filelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegtableh5mreadHDF5Arrayhighrhmshttrhttr2IlluminaHumanMethylation450kanno.ilmn12.hg19illuminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelifecyclelimmalocfitlumimagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimulttestnleqslvnlmenor1mixopensslorg.Hs.eg.dbpillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsROCRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsS7scalesscrimeselectrSeqinfosiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLxml2xtableXVectoryaml

The wateRmelon User's Guide

Tyler Gorrie-Stone, Leonard Schalkwyk

Rendered fromwateRmelon.Rmdusingknitr::rmarkdownon May 24 2026.

Last update: 2023-09-05
Started: 2023-09-04

Readme and manuals

Help Manual

Help pageTopics
Illumina 450K arrays: normalization and performance metricswateRmelon-package wateRmelon
Internal function to guess correct pData and retrieve using minfi.createAnnotation
Internal functions for Illumina i450 normalization functions.getManifestString fot got pop
Functions from 450-pipeline (Touleimat & Tost)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
adjustedDasenadjustedDasen
adjustedFunnormadjustedFunnorm
Age Prediction from methylomic expression dataagep agep,MethylSet-method agep,MethyLumiSet-method agep,RGChannelSet-method age_coefficients coef hannumCoef
Methods for Function 'as.methylumi'as.methylumi as.methylumi,ANY-method as.methylumi,MethylSet-method as.methylumi,MethyLumiSet-method as.methylumi-methods getColumns
Calculates the number of samples with bead count <3 for each probe in matrix of bead count valuesbeadc
Creates matrix of beacounts from minfi data.beadcount
Internal functions for peak.correction (fuks)Beta2M correctI correctII M2Beta summits
Calculate normalized betas from exprmethy450 of Illumina 450K methylation arraysbetaqn,exprmethy450-method fuks,exprmethy450-method
Beta-Mixture Quantile (BMIQ) Normalisation method for Illumina 450k arraysBMIQ BMIQ,ANY-method BMIQ,MethylSet-method BMIQ,MethyLumiSet-method BMIQ-methods CheckBMIQ
Calculate bisulphite conversionbscon bscon,MethyLumiSet-method bscon,RGChannelSet-method
canno - process csv manifest into annotation object for illumina methylation preprocessingcanno
Methods for Function 'colnames' in Package 'wateRmelon'colnames,MethyLumiSet-method colnames-methods
Combine MethyLumiSet objectscombo
Calculate normalized betas from Illumina 450K methylation arraysbetaqn danen danes danet dasen daten1 daten2 fuks nanes nanet nasen naten swan tost
Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arraysbetaqn,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
Calculate normalized betas from Illumina 450K methylation arraysbetaqn,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
Internal wateRmelon functions for calculating betasdb1 dfs2 dfsfit
Standard error of iDMR 450k array DNA methylation featuresdmrse dmrse_col dmrse_row
Methods for Function 'dmrse' in Package 'wateRmelon'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
Strip and subset EPICv2 data to work with legacy data and methodsepicv2clean epicv2clean.default epicv2clean.gds.class
Cell Proportion Estimation using wateRmelonestimateCellCounts.wateRmelon estimateCellCounts.wateRmelon,MethylSet-method estimateCellCounts.wateRmelon,MethyLumiSet-method estimateCellCounts.wateRmelon,RGChannelSet-method estimateCellCounts.wmln
Predict sex by using robust sex-related CpG sites on ChrX and ChrYestimateSex
SNP derived performance metrics for Illumina 450K DNA methylation arrays.genki
Methods for Function 'genki' in Package 'wateRmelon'genki,exprmethy450-method genki,MethylSet-method genki,MethyLumiSet-method genki,RGChannelSet-method genki-methods
Internal functions for genotype-based normalization metricsgcoms gcose genkme genkus getsnp
Internal functions for Illumina i450 normalization functionsfot got
idet - identify idats by a hash of the addressesidet
Imprinting differentially methylated region probes of Illumina 450 arraysiDMR
Small MethyLumi data set for examples and testingmelon
Calculate a full set of 450K normalization/performance metricsmetrics
For internal use, is read using minfi-like machinery and then preprocessed into the more flexible and convenient methylumi object used by wateRmelon/bigmelonNChannelSetToMethyLumiSet2
Identify Outliers within Methylumi and Minfi packaged objectsoutlyx
Methods for Function 'outlyx' in Package 'wateRmelon'outlyx,MethylSet-method outlyx,MethyLumiSet-method outlyx,RGChannelSet-method
Basic data filtering for Illumina 450 methylation datapfilter pfilter,MethyLumiSet-method pfilter,RGChannelSetExtended-method pfilter-methods
Probe-Wise Outlier Detectionpwod
Methods for Function 'pwod' in Package 'wateRmelon'pwod,MethylSet-method pwod,MethyLumiSet-method pwod,RGChannelSet-method
A measure of Normalization Violencequal
read.manifest - read in csv format Illumina chip manifest filesread.manifest
readEPICepic.controls readEPIC
readPepo - read (any kind of) Illumina DNA methylation array idat files into a methylumi objectreadPepo
Calculate a performance metric based on male-female differences for Illumina methylation 450K arraysseabi
Methods for Function 'seabi' in Package 'wateRmelon'seabi,exprmethy450-method seabi,MethylSet-method seabi,MethyLumiSet-method seabi,RGChannelSet-method seabi-methods
Calculate ROC area-under-curve for X-chromosome sex differences (internal function for calculating the seabi metric)seabird
Test Illumina methylation 450K array probes for sex difference (internal function for calculating 'seabi' performance metric)sextest
Smoking Prediction from methylomic expression datasmokp smokp,MethylSet-method smokp,MethyLumiSet-method smokp,RGChannelSet-method smokp_cpgs
Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1anSNP 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