Package: wateRmelon
Type: Package
Title: Illumina 450 methylation array normalization and metrics
Version: 1.37.0
Author: Leonard C Schalkwyk, Ruth Pidsley, Chloe CY Wong, with functions contributed by Nizar Touleimat, Matthieu Defrance, Andrew Teschendorff, Jovana Maksimovic, Tyler Gorrie-Stone, Louis El Khoury
Maintainer: Leo <lschal@essex.ac.uk>
Description: 15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.
License: GPL-3
Depends: R (>= 2.10), Biobase, limma, methods, matrixStats, methylumi,
        lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19,
        illuminaio
Imports: Biobase
Enhances: minfi
Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
        IlluminaHumanMethylationEPICmanifest, irlba
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
        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 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
        predictSex.R pwod.R readEPIC.R preprocessIlluminaMethylation.R
        referenceQuantiles.R
        robustQuantileNorm_Illumina450K.probeCategories.R
        robustQuantileNorm_Illumina450K.R seabird.R sextest.R summits.R
        swan2.R uniqueAnnotationCategory.R qual.R AllGenerics.R
        x_methylumi.R y_minfi.R
git_url: https://git.bioconductor.org/packages/wateRmelon
git_branch: master
git_last_commit: 094eaac
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19
NeedsCompilation: no
Packaged: 2021-05-20 03:07:32 UTC; biocbuild
Built: R 4.1.0; ; 2021-05-20 15:10:28 UTC; unix
