Package: mpactr 0.1.0

Patrick Schloss

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.

Authors:Allison Mason [aut], Gregory Johnson [aut], Patrick Schloss [aut, cre, cph]

mpactr_0.1.0.tar.gz
mpactr_0.1.0.tar.gz(r-4.5-noble)mpactr_0.1.0.tar.gz(r-4.4-noble)
mpactr_0.1.0.tgz(r-4.4-emscripten)mpactr_0.1.0.tgz(r-4.3-emscripten)
mpactr.pdf |mpactr.html
mpactr/json (API)
NEWS

# Install 'mpactr' in R:
install.packages('mpactr', repos = 'https://cloud.r-project.org')

Peer review:

Bug tracker:https://github.com/mums2/mpactr/issues

Pkgdown site:https://mums2.github.io

Datasets:

1.70 score 4 scripts 195 downloads 15 exports 57 dependencies

Last updated 4 months agofrom:6d6ff78ea8. Checks:2 OK. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKJan 09 2025
R-4.5-linuxOKJan 09 2025

Exports:examplefilter_cvfilter_groupfilter_insource_ionsfilter_mispicked_ionsfilter_summaryget_cv_dataget_group_averagesget_meta_dataget_peak_tableget_raw_dataget_similar_ionsimport_dataplot_qc_treeqc_summary

Dependencies:bitbit64clicliprcolorspacecommonmarkcpp11crayoncurldata.tablefansifarverggfittextggplot2gluegridExtragridtextgtablehmsisobandjpeglabelinglatticelifecyclemagrittrmarkdownMASSMatrixmgcvmunsellnlmepillarpkgconfigpngprettyunitsprogressR6RColorBrewerRcppreadrrlangscalesshadesstringistringrtibbletidyselecttreemapifytzdbutf8vctrsviridisviridisLitevroomwithrxfunxml2