Oshlack/missMethyl: Analysing Illumina HumanMethylation BeadChip Data

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.

Getting started

Package details

AuthorBelinda Phipson and Jovana Maksimovic
Bioconductor views DNAMethylation DifferentialMethylation GeneSetEnrichment GeneticVariability GenomicVariation MethylationArray Normalization
MaintainerBelinda Phipson <belinda.phipson@petermac.org>, Jovana Maksimovic <jovana.maksimovic@petermac.org>, Andrew Lonsdale <andrew.lonsdale@petermac.org>
LicenseGPL-2
Version1.23.2
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("Oshlack/missMethyl")
Oshlack/missMethyl documentation built on Sept. 29, 2020, 10:55 p.m.