Package: mpactr
Title: Correction of Preprocessed MS Data
Version: 0.1.0
Authors@R: c(
    person("Allison", "Mason", , "masonar@umich.edu", role = c("aut"),
            comment = c(ORCID = "0000-0003-1339-1592")),
    person("Gregory", "Johnson", , "grejoh@umich.edu", role = c("aut")),
    person("Patrick", "Schloss", , "pschloss@umich.edu", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0002-6935-4275"))
    )
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.2.9000
Suggests: testthat (>= 3.0.0)
Config/testthat/edition: 3
Depends: data.table, R (>= 4.1.0)
Imports: cli, ggplot2, R6, readr, stats, treemapify, viridis
LazyData: true
Config/Needs/website: rmarkdown, tidyverse, viridis, plotly, Hmisc,
        corrplot, ggdendro, ggtext
URL: https://mums2.github.io/mpactr/, https://github.com/mums2/mpactr
BugReports: https://github.com/mums2/mpactr/issues
NeedsCompilation: no
Packaged: 2024-09-05 20:36:10 UTC; masonar
Author: Allison Mason [aut] (<https://orcid.org/0000-0003-1339-1592>),
  Gregory Johnson [aut],
  Patrick Schloss [aut, cre, cph]
    (<https://orcid.org/0000-0002-6935-4275>)
Maintainer: Patrick Schloss <pschloss@umich.edu>
Repository: CRAN
Date/Publication: 2024-09-10 10:00:02 UTC
