missMethyl
Analysing Illumina HumanMethylation BeadChip Data
Bioconductor version: 3.23 · Package version: 1.46.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("missMethyl")Details
| 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> |
| Author | Belinda Phipson and Jovana Maksimovic |
| License | GPL-2 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, DifferentialMethylation, GeneSetEnrichment, GeneticVariability, GenomicVariation, MethylationArray, Normalization, Software |
| Package Short Url | https://bioconductor.org/packages/missMethyl/ |
Citation
From within R, enter citation("missMethyl"):
Belinda Phipson and Jovana Maksimovic. missMethyl: Analysing Illumina HumanMethylation BeadChip Data. doi:10.18129/B9.bioc.missMethyl, R package version 1.46.0, https://bioconductor.org/packages/missMethyl.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | missMethyl_1.46.0.tar.gz |
| Windows binary (x86_64) | missMethyl_1.46.0.zip |
| macOS binary (arm64) | missMethyl_1.46.0.tgz |
| macOS binary (x86_64) | missMethyl_1.46.0.tgz |
Dependencies
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
Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub