metaX: a flexible and comprehensive software for processing metabolomics data.
metaX: a flexible and comprehensive software for processing metabolomics data.
复制标题
DOI：
10.1186/s12859-017-1579-y
复制
发表时间：
2017-03-21
影响因子：
3
通讯作者：
Liu S
中科院分区：
文献类型：
--
作者：
Wen B;Mei Z;Zeng C;Liu S
基于质谱的非靶向代谢组学能够对生物样品中的代谢物进行高通量分析。质谱分析产生的大量数据需要进行密集的计算处理，以进行质谱注释和代谢物鉴定。这一研究领域需要具有多种功能的计算分析工具，即使用户缺乏广泛的编程知识，也能方便地操作。我们在此开发了一个R包metaX，它能够通过一组可互换的模块进行端到端的代谢组学数据分析。具体来说，metaX提供了几个功能，如峰采摘和注释、数据质量评估、缺失值输入、数据归一化、单变量和多变量统计、功率分析和样本量估计、接受者工作特征分析、生物标志物选择、途径注释、相关网络分析和代谢物鉴定。此外，metaX还提供基于web的数据质量评估和规范化方法评估界面（http://metax.genomics.cn），并生成基于html的可视化界面报告。metaX实用程序通过已发表的代谢组学数据集进行了大规模验证。该软件可作为基于web的图形用户界面（GUI）或命令行功能的形式进行操作。该包和示例报告可从http://metax.genomics.cn/获得。metaX的流水线是独立于平台的，易于用于分析质谱产生的代谢组学数据。本文的在线版本（doi:10.1186/s12859-017-1579-y）包含补充材料，授权用户可以使用。
Non-targeted metabolomics based on mass spectrometry enables high-throughput profiling of the metabolites in a biological sample. The large amount of data generated from mass spectrometry requires intensive computational processing for annotation of mass spectra and identification of metabolites. Computational analysis tools that are fully integrated with multiple functions and are easily operated by users who lack extensive knowledge in programing are needed in this research field. We herein developed an R package, metaX, that is capable of end-to-end metabolomics data analysis through a set of interchangeable modules. Specifically, metaX provides several functions, such as peak picking and annotation, data quality assessment, missing value imputation, data normalization, univariate and multivariate statistics, power analysis and sample size estimation, receiver operating characteristic analysis, biomarker selection, pathway annotation, correlation network analysis, and metabolite identification. In addition, metaX offers a web-based interface (http://metax.genomics.cn) for data quality assessment and normalization method evaluation, and it generates an HTML-based report with a visualized interface. The metaX utilities were demonstrated with a published metabolomics dataset on a large scale. The software is available for operation as either a web-based graphical user interface (GUI) or in the form of command line functions. The package and the example reports are available at http://metax.genomics.cn/. The pipeline of metaX is platform-independent and is easy to use for analysis of metabolomics data generated from mass spectrometry. The online version of this article (doi:10.1186/s12859-017-1579-y) contains supplementary material, which is available to authorized users.