Load required libraries | Filter MS1 feature table with mpactr | Interactive scatter plot of all input ions and their fate during filtering | Correlation between samples at different levels | Correlation between each individual sample | Correlation between technical replicates | Correlation between biological replicates | Dendrogram | Fold change analysis | Calculate fold change | Visualize fold change for compounds in a 3D scatter plot | Test for compounds with significant fold changes | Volcano plot
Package: mpactr 0.3.3.9000
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_0.3.3.9000.tar.gz
mpactr_0.3.3.9000.zip(r-4.7)mpactr_0.3.3.9000.zip(r-4.6)mpactr_0.3.3.9000.zip(r-4.5)
mpactr_0.3.3.9000.tgz(r-4.6-x86_64)mpactr_0.3.3.9000.tgz(r-4.6-arm64)mpactr_0.3.3.9000.tgz(r-4.5-x86_64)mpactr_0.3.3.9000.tgz(r-4.5-arm64)
mpactr_0.3.3.9000.tar.gz(r-4.7-arm64)mpactr_0.3.3.9000.tar.gz(r-4.7-x86_64)mpactr_0.3.3.9000.tar.gz(r-4.6-arm64)mpactr_0.3.3.9000.tar.gz(r-4.6-x86_64)
mpactr_0.3.3.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mpactr/json (API)
| # 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/docs site:https://www.mums2.org
Datasets:
- cultures_data - LC-MS/MS sample data
Last updated from:ccdf56506d. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 236 | ||
| linux-devel-x86_64 | OK | 268 | ||
| source / vignettes | OK | 291 | ||
| linux-release-arm64 | OK | 276 | ||
| linux-release-x86_64 | OK | 229 | ||
| macos-release-arm64 | OK | 171 | ||
| macos-release-x86_64 | OK | 410 | ||
| macos-oldrel-arm64 | OK | 154 | ||
| macos-oldrel-x86_64 | OK | 355 | ||
| windows-devel | OK | 164 | ||
| windows-release | OK | 168 | ||
| windows-oldrel | OK | 180 | ||
| wasm-release | OK | 213 |
Exports:example_pathfilter_cvfilter_groupfilter_insource_ionsfilter_mispicked_ionsfilter_summaryget_cv_dataget_group_averagesget_metadataget_peak_tableget_raw_dataget_similar_ionsimport_datalimit_coresplot_qc_treeqc_summary
Dependencies:base64encclicommonmarkcpp11curldata.tablefarverggfittextggplot2gluegridExtragridtextgtableisobandjpegjsonlitelabelinglifecyclelitedownmagrittrmarkdownpngR6RColorBrewerRcpprlangS7scalesshadesstringistringrsvglitesystemfontstextshapingtreemapifyvctrsviridisviridisLitewithrxfunxml2
Downstream Analyses
Last update: 2026-05-20
Started: 2024-11-26
Filter with mpact original data
Load data into R | Accessing data in mpactr object | Extract peak table | Extract metadata | Reference semantics | Filtering | Mispicked ions filter | Remove ions that are above a threshold in one biological group | Remove non-reproducible ions | Remove insource fragment ions | Chaining filters together | Summary | View passing and failed ions for a single filter | View passing and failed ions for all input ions | Visualize filtering QC with tree map plot
Last update: 2026-05-20
Started: 2024-11-26
Reference Semantics
Reference semantics | Deep copy: specifics of the R6 class
Last update: 2026-05-15
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_metadata |
| 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 |
| Limit Cores | limit_cores |
| Visualize Filtering Summary as Tree Map | plot_qc_tree |
| Summary of Filtering | qc_summary |
