missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform

Belinda Phipson; Jovana Maksimovic; Alicia Oshlack

doi:10.1093/bioinformatics/btv560

missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform

Bioinformatics. 2016 Jan 15;32(2):286-8. doi: 10.1093/bioinformatics/btv560. Epub 2015 Sep 30.

Authors

Belinda Phipson¹, Jovana Maksimovic¹, Alicia Oshlack¹

Affiliation

¹ Bioinformatics Group, Murdoch Childrens Research Institute, Royal Children's Hospital, 50 Flemington Road, Parkville, Victoria, 3052, Australia.

PMID: 26424855
DOI: 10.1093/bioinformatics/btv560

Abstract

DNA methylation is one of the most commonly studied epigenetic modifications due to its role in both disease and development. The Illumina HumanMethylation450 BeadChip is a cost-effective way to profile >450 000 CpGs across the human genome, making it a popular platform for profiling DNA methylation. Here we introduce missMethyl, an R package with a suite of tools for performing normalization, removal of unwanted variation in differential methylation analysis, differential variability testing and gene set analysis for the 450K array.

Availability and implementation: missMethyl is an R package available from the Bioconductor project at www.bioconductor.org.

Contact: alicia.oshlack@mcri.edu.au

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods*
CpG Islands
DNA Methylation*
Genome, Human*
Humans
Oligonucleotide Array Sequence Analysis / methods*
Software*