ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
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DOI：
10.1093/bioinformatics/btp508
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发表时间：
2009-10-15
期刊：
影响因子：
5.8
通讯作者：
Dalevi, Daniel
中科院分区：
文献类型：
--
作者：
Kristiansson, Erik;Hugenholtz, Philip;Dalevi, Daniel
微生物在自然界中无处不在，几乎构成每个生态系统的固有部分。宏基因组学是研究微生物群落的一种不依赖于培养的强有力的方法。在这类研究中，对群落中多个物种的片段化遗传物质进行功能分析。高通量测序的最新进展极大地增加了宏基因组项目中的数据量。目前，迫切需要有效的统计工具来分析这些数据。我们已经创建了ShotgunFunctionalizeR，这是一个用于宏基因组功能比较的R软件包。该软件包包含用于导入、注释和可视化由鸟枪法高通量测序产生的宏基因组数据的工具。ShotgunFunctionalizeR包含几个统计程序，用于评估样本之间的功能差异，包括单个基因和整个途径。除了标准和以前公布的方法，我们已经开发和实施了一种新的方法的基础上泊松模型。该方法非常灵活，因此适用于各种不同的实验设计。我们通过对在太平洋多个深度采样的宏基因组进行回归分析来证明ShotgunFunctionalizeR的潜力。
Microorganisms are ubiquitous in nature and constitute intrinsic parts of almost every ecosystem. A culture-independent and powerful way to study microbial communities is metagenomics. In such studies, functional analysis is performed on fragmented genetic material from multiple species in the community. The recent advances in high-throughput sequencing have greatly increased the amount of data in metagenomic projects. At present, there is an urgent need for efficient statistical tools to analyse these data. We have created ShotgunFunctionalizeR, an R-package for functional comparison of metagenomes. The package contains tools for importing, annotating and visualizing metagenomic data produced by shotgun high-throughput sequencing. ShotgunFunctionalizeR contains several statistical procedures for assessing functional differences between samples, both for individual genes and for entire pathways. In addition to standard and previously published methods, we have developed and implemented a novel approach based on a Poisson model. This procedure is highly flexible and thus applicable to a wide range of different experimental designs. We demonstrate the potential of ShotgunFunctionalizeR by performing a regression analysis on metagenomes sampled at multiple depths in the Pacific Ocean.