DOI: 10.18129/B9.bioc.missMethyl  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see missMethyl.

Analysing Illumina HumanMethylation BeadChip Data

Bioconductor version: 3.16

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.

Author: Belinda Phipson and Jovana Maksimovic

Maintainer: Belinda Phipson <belinda.phipson at petermac.org>, Jovana Maksimovic <jovana.maksimovic at petermac.org>, Andrew Lonsdale <andrew.lonsdale at petermac.org>

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biocViews DNAMethylation, DifferentialMethylation, GeneSetEnrichment, GeneticVariability, GenomicVariation, MethylationArray, Normalization, Software
Version 1.32.1
In Bioconductor since BioC 3.0 (R-3.1) (8.5 years)
License GPL-2
Depends R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Imports AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment
Suggests BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub
Depends On Me methylationArrayAnalysis
Imports Me ChAMP, DMRcate, MEAL, methylGSA
Suggests Me RnBeads
Links To Me
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