ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data
The high-resolution and mass accuracy of Fourier transform mass spectrometry (FT-MS) has made it an increasingly popular technique for discerning the composition of soil, plant and aquatic samples containing complex mixtures of proteins, carbohydrates, lipids, lignins, hydrocarbons, phytochemicals a...
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| Veröffentlicht in: | PLoS computational biology 2020-03, Vol.16 (3), p.e1007654-e1007654 |
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| creator | Bramer, Lisa M White, Amanda M Stratton, Kelly G Thompson, Allison M Claborne, Daniel Hofmockel, Kirsten McCue, Lee Ann |
| description | The high-resolution and mass accuracy of Fourier transform mass spectrometry (FT-MS) has made it an increasingly popular technique for discerning the composition of soil, plant and aquatic samples containing complex mixtures of proteins, carbohydrates, lipids, lignins, hydrocarbons, phytochemicals and other compounds. Thus, there is a growing demand for informatics tools to analyze FT-MS data that will aid investigators seeking to understand the availability of carbon compounds to biotic and abiotic oxidation and to compare fundamental chemical properties of complex samples across groups. We present ftmsRanalysis, an R package which provides an extensive collection of data formatting and processing, filtering, visualization, and sample and group comparison functionalities. The package provides a suite of plotting methods and enables expedient, flexible and interactive visualization of complex datasets through functions which link to a powerful and interactive visualization user interface, Trelliscope. Example analysis using FT-MS data from a soil microbiology study demonstrates the core functionality of the package and highlights the capabilities for producing interactive visualizations. |
| doi_str_mv | 10.1371/journal.pcbi.1007654 |
| format | Article |
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| subjects | Aquatic plants Biology and Life Sciences Carbohydrates Carbon Carbon compounds Chemical properties Computer and Information Sciences Data analysis Data collection Data processing Datasets Engineering and Technology Fourier analysis Fourier transforms Informatics Laboratories Lipids Mass spectrometry Mass spectroscopy Microbiology Open source software Oxidation Oxidation-reduction reactions Physical Sciences Proteins Research and Analysis Methods Researchers Scientific imaging Soil microbiology Soils Spectroscopy Visualization Visualization (Computer) |
| title | ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data |
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