Package: missMethyl
Type: Package
Title: Analysing Illumina HumanMethylation BeadChip Data
Version: 1.45.0
Date: 2025-09-08
Author: Belinda Phipson and Jovana Maksimovic
Maintainer: Belinda Phipson <phipson.b@wehi.edu.au>, Jovana Maksimovic
 <jovana.maksimovic@petermac.org>, Andrew Lonsdale
 <andrew.lonsdale@petermac.org>, Calandra Grima
 <calandra.grima@petermac.org>
Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
        IlluminaHumanMethylationEPICv2anno.20a1.hg38
Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomeInfoDb,
        GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest,
        IlluminaHumanMethylationEPICmanifest,
        IlluminaHumanMethylationEPICv2manifest, IRanges, limma,
        methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors,
        statmod, stringr, SummarizedExperiment
VignetteBuilder: knitr
Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown,
        tweeDEseqCountData, DMRcate, ExperimentHub
Description: Normalisation, testing for differential variability and
        differential methylation and gene set testing for data from
        Illumina's Infinium HumanMethylation arrays. The normalisation
        procedure is subset-quantile within-array normalisation (SWAN),
        which allows Infinium I and II type probes on a single array to
        be normalised together. The test for differential variability
        is based on an empirical Bayes version of Levene's test.
        Differential methylation testing is performed using RUV, which
        can adjust for systematic errors of unknown origin in
        high-dimensional data by using negative control probes. Gene
        ontology analysis is performed by taking into account the
        number of probes per gene on the array, as well as taking into
        account multi-gene associated probes.
License: GPL-2
biocViews: Normalization, DNAMethylation, MethylationArray,
        GenomicVariation, GeneticVariability, DifferentialMethylation,
        GeneSetEnrichment
RoxygenNote: 7.3.3
Encoding: UTF-8
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:20:32 UTC
RemoteUrl: https://github.com/bioc/missMethyl
RemoteRef: HEAD
RemoteSha: 886b6567450362ec06e1f1a36a5e78f43fde4232
NeedsCompilation: no
Packaged: 2025-10-30 07:57:48 UTC; root
Built: R 4.6.0; ; 2025-10-30 08:17:10 UTC; windows
