Bottomly Daniel, Wilmot Beth, McWeeney Shannon K
Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US.
BMC Bioinformatics. 2015 Apr 29;16(1):134. doi: 10.1186/s12859-015-0547-7.
Characterization of respiratory phenotypes can enhance complex trait and genomic studies involving allergic/autoimmune and infectious diseases. Many aspects of respiration can be measured using devices known as plethysmographs that can measure thoracic movement. One such approach (the Buxco platform) performs unrestrained whole body plethysmography on mice which infers thoracic movements from pressure differences from the act of inhalation and exhalation. While proprietary software is available to perform basic statistical analysis as part of machine's bundled software, it is desirable to be able to incorporate these analyses into high-throughput pipelines and integrate them with other data types, as well as leverage the wealth of analytic and visualization approaches provided by the R statistical computing environment.
This manuscript describes the plethy package which is an R/Bioconductor framework for pre-processing and analysis of plethysmography data with emphasis on larger scale longitudinal experiments. The plethy package was designed to facilitate quality control and exploratory data analysis. We provide a demonstration of the features of plethy using a dataset assessing the respiratory effects over time of SARS and Influenza infection in mice.
The plethy package provides functionality for users to import, perform quality assessment and exploratory data analysis in a manner that allows interoperability with existing modelling tools. Our package is implemented in R and is freely available as part of the Bioconductor project http://www.bioconductor.org/packages/release/bioc/html/plethy.html .
呼吸表型的特征描述可加强涉及过敏性/自身免疫性疾病和感染性疾病的复杂性状及基因组研究。呼吸的许多方面可以使用称为体积描记器的设备进行测量，该设备可测量胸部运动。一种这样的方法（Buxco平台）对小鼠进行无限制的全身体积描记，通过吸入和呼气动作产生的压力差来推断胸部运动。虽然作为机器捆绑软件的一部分，有专有软件可用于执行基本统计分析，但希望能够将这些分析纳入高通量流程，并将它们与其他数据类型集成，同时利用R统计计算环境提供的丰富分析和可视化方法。
本文描述了plethy软件包，它是一个R/Bioconductor框架，用于体积描记数据的预处理和分析，重点是大规模纵向实验。plethy软件包旨在促进质量控制和探索性数据分析。我们使用一个评估小鼠感染SARS和流感后随时间变化的呼吸效应的数据集，展示了plethy的功能。
plethy软件包为用户提供了导入、进行质量评估和探索性数据分析的功能，其方式允许与现有建模工具进行互操作。我们的软件包是用R实现的，可作为Bioconductor项目的一部分免费获取，网址为http://www.bioconductor.org/packages/release/bioc/html/plethy.html 。
