DESCRIPTION

Package: wateRmelon
Type: Package
Title: Illumina DNA methylation array normalization and metrics
Version: 2.11.4
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