plethy: management of whole body plethysmography data in R.
BACKGROUND
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.


RESULTS
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.


CONCLUSIONS
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 .
Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US. bottomly@ohsu.edu.
Daniel
D
Bottomly
Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US. wilmotb@ohsu.edu.
Beth
B
Wilmot
Oregon Clinical and Translational Research Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd97239, Portland, Oregon, US. mcweeney@ohsu.edu.
Shannon K
SK
McWeeney
D000818:Animals; D001717:Birds; D003196:Computer Graphics; D017934:Coronavirus / Q000235:genetics; D016679:Genome, Viral; D023281:Genomics; D009980:Influenza A virus / Q000235:genetics; D005585:Influenza in Birds / Q000821:virology; D051379:Mice; D008810:Mice, Inbred C57BL; D015233:Models, Statistical; D009976:Orthomyxoviridae Infections / Q000821:virology; D010641:Phenotype; D010993:Plethysmography, Whole Body; D012119:Respiration / Q000235:genetics*; D045169:Severe Acute Respiratory Syndrome / Q000821:virology; D012984:Software