pmartR
This R package provides functionality for quality control processing, statistical analysis and visualization of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level; isobaric labeled or unlabled), lipidomic, and metabolomic data. This includes data transformation, specification of groups that are to be compared against each other, filtering of feature and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons of groups of interest (ANOVA and/or independence of missing data tests). Example data to be used with this packages can be found in pmartRdata.
Installation:
devtools::install_github("pmartR/pmartR")Tutorial:
To get started, see the package documentation and function reference located here.
Data:
Example peptide (both unlabeled and isobaric labeled), protein, metabolite and lipid data are available in the pmartRdata package available on Github, here
Citation:
To cite this package, please use the following:
Stratton KG, Webb-Robertson BJ, McCue LA, Stanfill B, Claborne D, Godinez I, Johansen T, Thompson AM, Burnum-Johnson KE, Waters KM, Bramer LM. pmartR: quality control and statistics for mass spectrometry-based biological data. Journal of proteome research. 2019 Jan 14;18(3):1418-25.