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MethParquet: an R package for rapid and efficient DNA methylation association analysis adopting Apache Parquet.
Ziqing Wang1, Michael Cassidy1, Danielle A Wallace1,2,3,4
1Department of Medicine, Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA, 02215, United States.
Bioinformatics (Oxford, England)
|June 19, 2024
Summary
MethParquet is a new R package that uses the efficient Parquet format to speed up the analysis of large genome-wide DNA methylation datasets. This tool reduces computational challenges in epigenome-wide association studies (EWAS) and methylation risk score calculations.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Genome-wide DNA methylation (DNAm) profiling is crucial for understanding biological pathways and individual phenotypes.
- Analyzing large-scale DNAm data from cohort studies faces significant computational challenges.
- Conventional row-based data formats hinder efficient storage, retrieval, and manipulation of extensive DNAm datasets.
Purpose of the Study:
- Introduce MethParquet, the first R package designed for efficient DNAm data analysis using the columnar Parquet format.
- Provide a computational solution to manage and analyze large DNAm datasets.
- Facilitate standard post-quality control tasks in DNAm research.
Main Methods:
- Leveraging the Apache Parquet columnar storage format within an R package.
- Implementing functionalities for data extraction, methylation risk score calculation, and epigenome-wide association studies (EWAS).
- Supporting diverse regression models for flexible analysis.
Main Results:
- Demonstrated significant reductions in running time and RAM usage for large-scale EWAS.
- Validated the efficiency of MethParquet using a public methylation dataset.
- Established MethParquet as a tool for efficient DNAm data analysis.
Conclusions:
- MethParquet effectively addresses computational obstacles in large-scale DNAm data analysis.
- The package enhances the efficiency of standard post-quality control tasks in EWAS.
- MethParquet offers a valuable resource for researchers working with extensive DNA methylation datasets.
