Package: mpactr
Title: Correction of Preprocessed MS Data
Version: 0.3.3.9000
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"),
            comment = c(ORCID = "0009-0008-3890-0297")),
    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.
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), tidyverse, plotly,
        Hmisc, corrplot, ggdendro, ggtext
Config/testthat/edition: 3
Imports: cli, data.table, ggplot2, R6, Rcpp, stats, treemapify, viridis
LazyData: true
URL: https://www.mums2.org/mpactr/, https://github.com/mums2/mpactr
BugReports: https://github.com/mums2/mpactr/issues
VignetteBuilder: knitr
LinkingTo: Rcpp
License: GPL (>= 3)
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libfribidi-dev
        libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libxml2-dev
        libssl-dev
Repository: https://mums2.r-universe.dev
Date/Publication: 2026-05-21 19:28:37 UTC
RemoteUrl: https://github.com/mums2/mpactr
RemoteRef: HEAD
RemoteSha: ccdf56506ddf6d66f72440f84e2046e90493ddb7
NeedsCompilation: yes
Packaged: 2026-06-24 12:59:29 UTC; root
Author: Allison Mason [aut] (ORCID: <https://orcid.org/0000-0003-1339-1592>),
  Gregory Johnson [aut] (ORCID: <https://orcid.org/0009-0008-3890-0297>),
  Patrick Schloss [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-6935-4275>)
Maintainer: Patrick Schloss <pschloss@umich.edu>
Depends: R (>= 3.5.0)