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:
mpactr_0.1.0.tar.gz
mpactr_0.1.0.zip(r-4.5)mpactr_0.1.0.zip(r-4.4)mpactr_0.1.0.zip(r-4.3)
mpactr_0.1.0.tgz(r-4.5-any)mpactr_0.1.0.tgz(r-4.4-any)mpactr_0.1.0.tgz(r-4.3-any)
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 = c('https://mums2.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mums2/mpactr/issues
Pkgdown site:https://www.mums2.org
- cultures_data - LC-MS/MS sample data
Last updated 25 days agofrom:01f5082dd6. Checks:8 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 13 2025 |
| R-4.5-win | OK | Feb 13 2025 |
| R-4.5-mac | OK | Feb 13 2025 |
| R-4.5-linux | OK | Feb 13 2025 |
| R-4.4-win | OK | Feb 13 2025 |
| R-4.4-mac | OK | Feb 13 2025 |
| R-4.3-win | OK | Feb 13 2025 |
| R-4.3-mac | OK | Feb 13 2025 |
Exports:example_pathfilter_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
Downstream Analyses
Rendered fromdownstream_analyses.Rmdusingknitr::rmarkdownon Feb 13 2025.Last update: 2024-11-26
Started: 2024-11-26
Filter with mpact original data
Rendered frommpactr.Rmdusingknitr::rmarkdownon Feb 13 2025.Last update: 2024-11-26
Started: 2024-11-26
Reference Semantics
Rendered fromreference_semantics.Rmdusingknitr::rmarkdownon Feb 13 2025.Last update: 2024-11-26
Started: 2024-11-26
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| LC-MS/MS sample data | cultures_data |
| Get file paths for examples | example_path |
| Filter Non-reproducible ions | filter_cv |
| Filter Ions by Group | filter_group |
| Filter Insource ions | filter_insource_ions |
| Mispicked ions filter | filter_mispicked_ions |
| Return the summary for a single mpactr filter. | filter_summary |
| Get CV values. | get_cv_data |
| Get groups averages. | get_group_averages |
| Return the meta_data data.table from the mpactr object. | get_meta_data |
| Return the peak table data.table from the mpactr object. | get_peak_table |
| Return the input peak table from mpactr object. | get_raw_data |
| Get similar ion groups. | get_similar_ions |
| Import data into an mpactr object. | import_data |
| Visualize Filtering Summary as Tree Map | plot_qc_tree |
| Summary of Fitering | qc_summary |
