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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("missMethyl")
In most cases, you don't need to download the package archive at all.
missMethyl
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see missMethyl.
Analysing Illumina HumanMethylation BeadChip Data
Bioconductor version: 3.4
Normalisation and testing for differential variability and differential methylation for data from Illumina's Infinium HumanMethylation450 array. 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.
Author: Belinda Phipson and Jovana Maksimovic
Maintainer: Belinda Phipson <belinda.phipson at mcri.edu.au>, Jovana Maksimovic <jovana.maksimovic at mcri.edu.au>
Citation (from within R,
enter citation("missMethyl")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("missMethyl")
Documentation
| HTML | R Script | missMethyl: Analysing Illumina HumanMethylation BeadChip Data |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DNAMethylation, DifferentialMethylation, GeneSetEnrichment, GeneticVariability, GenomicVariation, MethylationArray, Normalization, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2.5 years) |
| License | GPL-2 |
| Depends | R (>= 2.3.0) |
| Imports | limma, minfi, methylumi, IlluminaHumanMethylation450kmanifest, statmod, ruv, stringr, IlluminaHumanMethylation450kanno.ilmn12.hg19, org.Hs.eg.db, AnnotationDbi, BiasedUrn, GO.db, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 |
| LinkingTo | |
| Suggests | minfiData, BiocStyle, knitr, rmarkdown, edgeR, tweeDEseqCountData |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | DMRcate |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | missMethyl_1.8.0.tar.gz |
| Windows Binary | missMethyl_1.8.0.zip |
| Mac OS X 10.9 (Mavericks) | missMethyl_1.8.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/missMethyl/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/missMethyl/ |
| Package Downloads Report | Download Stats |
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