MethylCallR : a comprehensive analysis framework for Illumina Methylation Beadchip.

IF 3.8 2区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Scientific Reports Pub Date : 2024-11-07 DOI:10.1038/s41598-024-77914-5

Hyun-Ho Yang, Mi-Ryung Han

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Abstract

DNA methylation is a molecular process that mediates gene-environment interactions. Epigenome-wide association studies (EWAS) using the Illumina Human Methylation BeadChip are powerful tools for quantifying the relationship between DNA methylation and phenotypes. Recently, the Illumina Methylation EPICv2 BeadChip (EPICv2) was released, which includes new features, such as duplicated probes and changed probe names. Several published algorithms have been updated to address these features in EPICv2. However, appropriate EPICv2 preprocessing and integration with previous microarray versions remain complex. Therefore, MethylCallR, an open-source R package designed to provide standard procedures for performing EWAS using Illumina methylation microarrays including EPICv2, was developed. MethylCallR can be used to control duplicated probes in EPICv2, by using pre-set data implemented in MethylCallR or new customized data. MethylCallR includes a straightforward conversion function between different types of Illumina Human Methylation BeadChips. Using MethylCallR, potential outlier sample detection and statistical power estimation were conducted and used to select meaningful probes. Publicly available data was analyzed using MethylCallR and the findings were compared to that of a previous study.

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MethylCallR：Illumina甲基化芯片的综合分析框架。

DNA 甲基化是介导基因与环境相互作用的分子过程。利用 Illumina 人类甲基化芯片进行的全表观基因组关联研究（EWAS）是量化 DNA 甲基化与表型之间关系的有力工具。最近，Illumina 发布了甲基化 EPICv2 芯片（EPICv2），其中包括一些新功能，如重复探针和更改探针名称。然而，适当的 EPICv2 预处理以及与以前微阵列版本的整合仍然很复杂。因此，MethylCallR 应运而生，它是一个开源 R 软件包，旨在为使用包括 EPICv2 在内的 Illumina 甲基化微阵列执行 EWAS 提供标准程序。MethylCallR 可用于控制 EPICv2 中的重复探针，方法是使用 MethylCallR 中的预设数据或新的定制数据。MethylCallR 包括不同类型 Illumina 人类甲基化芯片之间的直接转换功能。利用 MethylCallR，可以进行潜在离群样本检测和统计能力估计，并用于选择有意义的探针。使用 MethylCallR 对公开数据进行了分析，并将分析结果与之前的一项研究结果进行了比较。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Scientific Reports Natural Science Disciplines-

CiteScore

7.50

自引率

4.30%

发文量

19567

审稿时长

3.9 months

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