mpactr: Correction of Preprocessed MS Data
An 'R' implementation of the 'python' program Metabolomics Peak Analysis Computational Tool ('MPACT') (Robert M. Samples, Sara P. Puckett, and Marcy J. Balunas (2023) <doi:10.1021/acs.analchem.2c04632>). Filters in the package serve to address common errors in tandem mass spectrometry preprocessing, including: (1) isotopic patterns that are incorrectly split during preprocessing, (2) features present in solvent blanks due to carryover between samples, (3) features whose abundance is greater than user-defined abundance threshold in a specific group of samples, for example media blanks, (4) ions that are inconsistent between technical replicates, and (5) in-source fragment ions created during ionization before fragmentation in the tandem mass spectrometry workflow.
| Version: |
0.1.0 |
| Depends: |
data.table, R (≥ 4.1.0) |
| Imports: |
cli, ggplot2, R6, readr, stats, treemapify, viridis |
| Suggests: |
testthat (≥ 3.0.0) |
| Published: |
2024-09-10 |
| DOI: |
10.32614/CRAN.package.mpactr |
| Author: |
Allison Mason 
[aut],
Gregory Johnson [aut],
Patrick Schloss
[aut, cre, cph] |
| Maintainer: |
Patrick Schloss <pschloss at umich.edu> |
| BugReports: |
https://github.com/mums2/mpactr/issues |
| License: |
MIT + file LICENSE |
| URL: |
https://mums2.github.io/mpactr/, https://github.com/mums2/mpactr |
| NeedsCompilation: |
no |
| Materials: |
README NEWS |
| CRAN checks: |
mpactr results |
Documentation:
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