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

TLDR

DNA methylation is a key epigenetic modification studied in disease and development, and the Illumina HumanMethylation450 BeadChip offers a cost‑effective way to profile over 450,000 CpGs across the genome. missMethyl is an R package that supplies tools for normalization, removal of unwanted variation, differential variability testing, and gene‑set analysis of 450K array data. It is available from Bioconductor at www.bioconductor.org. Contact: [e-mail]; supplementary data are available online.

Abstract

Abstract Summary: 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: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.