Package: wateRmelon
Type: Package
Title: Illumina DNA methylation array normalization and metrics
Version: 2.15.0
Authors@R: c(person(c("Leo", "C"), "Schalkwyk", role = c("cre", "aut"),
                    email = "lschal@essex.ac.uk"),
             person(c("Tyler", "J"), "Gorrie-Stone", role = "aut"),
             person(c("Ruth"), "Pidsley", role = "aut"),
             person(c("Chloe", "CY"), "Wong", role = "aut"),
             person(c("Nizar"), "Touleimat", role='ctb'),
             person(c("Matthieu"), "Defrance", role='ctb'),
             person(c("Andrew"), "Teschendorff", role='ctb'),
             person(c("Jovana"), "Maksimovic", role='ctb'),
             person(c("Louis", "Y"), "El Khoury", role='ctb'),
             person(c("Yucheng"), "Wang", role='ctb'),
             person(c("Alexandria"), "Andrayas", role='ctb')
             )
Description: 15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.
License: GPL-3
Depends: R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi,
        lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19,
        illuminaio
Imports: Biobase
Enhances: minfi
Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
        BiocStyle, knitr, rmarkdown,
        IlluminaHumanMethylationEPICmanifest, irlba,
        FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore
LazyLoad: yes
biocViews: DNAMethylation, Microarray, TwoChannel, Preprocessing,
        QualityControl
Collate: as.methylumi.R bscon.R bscon_methy.R bscon_minfi.R getAnn.R
        oxyscale.R adaptRefQuantiles.R beta1.R Beta2M.R betaqn.R bgeq.R
        bgeqot.R bgeqq2.R bgeqqn.R BMIQ_1.1.R combo.R
        createAnnotation.R concatenateMatrices.R coRankedMatrices.R
        correctI.R correctII.R dataDetectPval2NA.R db1.R
        detectionPval.filter.R dfs2.R dfsfit.R dmrse.R dmrse_col.R
        dmrse_row.R dyebuy1.R dyebuy2.R dyebuy3.R dyebuy4.R
        estimateCellCounts.R estimateSex.R filterXY.R
        findAnnotationProbes.R gcoms.R gcose.R genki.R genkme.R
        genkus.R genotype.R getMethylumiBeta.R getQuantiles.R
        getSamples.R getsnp.R horv.R loadMethylumi2.R lumiMethyR2.R
        M2Beta.R melon.R nbBeadsFilter.R normalize.quantiles2.R
        normalizeIlluminaMethylation.R ot.R outlyx.R pasteque.R
        peak.correction.R pfilter.R pipelineIlluminaMethylation.batch.R
        pwod.R detection.R readEPIC.R preprocessIlluminaMethylation.R
        referenceQuantiles.R adjustedDasen.R adjustedFunnorm.R
        robustQuantileNorm_Illumina450K.probeCategories.R
        robustQuantileNorm_Illumina450K.R seabird.R sextest.R summits.R
        swan2.R uniqueAnnotationCategory.R qual.R uSexQN.R smokp.R
        manifesto.R readAny.R AllGenerics.R x_methylumi.R y_minfi.R
        z_bigmelon.R
RoxygenNote: 7.3.1
NeedsCompilation: no
VignetteBuilder: knitr
Encoding: UTF-8
git_url: https://git.bioconductor.org/packages/wateRmelon
git_branch: devel
git_last_commit: cf57c1a
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
Packaged: 2025-06-05 02:50:02 UTC; biocbuild
Author: 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]
Maintainer: Leo C Schalkwyk <lschal@essex.ac.uk>
Built: R 4.5.0; ; 2025-06-05 14:18:28 UTC; windows
