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missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform
Belinda Phipson1, Jovana Maksimovic1, Alicia Oshlack1
1Bioinformatics Group, Murdoch Childrens Research Institute, Royal Children's Hospital, 50 Flemington Road, Parkville, Victoria, 3052, Australia.
Bioinformatics (Oxford, England)
|October 2, 2015
Summary
This study introduces missMethyl, an R package for DNA methylation analysis using the Illumina HumanMethylation450 BeadChip. It offers tools for normalization, variation removal, and differential methylation analysis, aiding research in disease and development.
Area of Science:
- Epigenetics and Genomics
- Bioinformatics and Computational Biology
Background:
- DNA methylation is a key epigenetic modification crucial for development and disease.
- The Illumina HumanMethylation450 BeadChip is widely used for genome-wide DNA methylation profiling.
- Analysis of large-scale methylation data presents computational challenges.
Purpose of the Study:
- To introduce missMethyl, an R package designed for DNA methylation data analysis.
- To provide tools for normalization, removal of unwanted variation, and differential methylation analysis.
- To facilitate gene set analysis for the Illumina 450K array.
Main Methods:
- Development of an R package named missMethyl.
- Implementation of functions for data normalization and quality control.
- Inclusion of methods for differential methylation and variability testing.
- Integration of gene set analysis capabilities.
Main Results:
- missMethyl provides a comprehensive suite of tools for analyzing Illumina 450K methylation data.
- The package addresses common challenges in differential methylation analysis.
- It enables efficient processing and interpretation of large-scale epigenetic datasets.
Conclusions:
- missMethyl simplifies and enhances DNA methylation data analysis.
- The package supports researchers in identifying methylation patterns related to disease and development.
- It is a valuable resource for the bioinformatics community, available via Bioconductor.
