Add MZMine metabolomics vignette and re-export MZMinetoMSstatsFormat#211
Add MZMine metabolomics vignette and re-export MZMinetoMSstatsFormat#211swaraj-neu wants to merge 2 commits into
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No actionable comments were generated in the recent review. 🎉 ℹ️ Recent review info⚙️ Run configurationConfiguration used: Organization UI Review profile: CHILL Plan: Pro Run ID: 📒 Files selected for processing (1)
🚧 Files skipped from review as they are similar to previous changes (1)
📝 WalkthroughWalkthrough
ChangesMZMinetoMSstatsFormat re-export and metabolomics vignette
Sequence Diagram(s)sequenceDiagram
participant User
participant MSstatsConvert
participant MSstats
User->>MSstatsConvert: system.file() — retrieve MZMine, annotation, library, SIRIUS CSVs
User->>MSstatsConvert: MZMinetoMSstatsFormat(mzmine, annotation, library, sirius)
MSstatsConvert-->>User: MSstats-format data frame
User->>MSstats: dataProcess(converted, logTrans=2, normalization="equalizeMedians", MBimpute=TRUE)
MSstats-->>User: FeatureLevelData + ProteinLevelData
User->>MSstats: groupComparison(contrast.matrix, summarized)
MSstats-->>User: ComparisonResult (log2FC, pvalue, adj.pvalue, issue)
User->>MSstats: dataProcessPlots(type="ProfilePlot")
User->>MSstats: groupComparisonPlots(type="VolcanoPlot", eval=FALSE)
Estimated code review effort🎯 2 (Simple) | ⏱️ ~12 minutes Poem
🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
✏️ Tip: You can configure your own custom pre-merge checks in the settings. ✨ Finishing Touches🧪 Generate unit tests (beta)
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🧹 Nitpick comments (1)
vignettes/MSstatsMetabolomics.Rmd (1)
39-39: 💤 Low valueConsider adding a reference for the MSI levels citation.
Line 39 references "Sumner et al., 2007" for the MSI (Metabolomics Standards Initiative) identification levels. While informal citations are acceptable in vignettes, adding a brief reference or URL would help readers locate the source document if they want to learn more about the classification system.
📚 Optional addition
You could add a references section at the end:
## __References__ Sumner, L.W., Amberg, A., Barrett, D., et al. (2007). Proposed minimum reporting standards for chemical analysis. _Metabolomics_, 3, 211-221. https://doi.org/10.1007/s11306-007-0082-2Or simply add the DOI inline:
- correspond to MSI Level 2 putative identifications (Sumner et al., 2007). + correspond to MSI Level 2 putative identifications (Sumner et al., 2007, https://doi.org/10.1007/s11306-007-0082-2).🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@vignettes/MSstatsMetabolomics.Rmd` at line 39, Add a formal reference for the Sumner et al., 2007 citation mentioned in relation to MSI Level 2 identification levels. Either create a References section at the end of the vignette document with the complete citation details (authors, year, title, journal, volume, pages, and DOI), or add the DOI inline with the existing citation at the location where MSI levels are mentioned. This will help readers locate the source document and understand the classification system better.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Nitpick comments:
In `@vignettes/MSstatsMetabolomics.Rmd`:
- Line 39: Add a formal reference for the Sumner et al., 2007 citation mentioned
in relation to MSI Level 2 identification levels. Either create a References
section at the end of the vignette document with the complete citation details
(authors, year, title, journal, volume, pages, and DOI), or add the DOI inline
with the existing citation at the location where MSI levels are mentioned. This
will help readers locate the source document and understand the classification
system better.
ℹ️ Review info
⚙️ Run configuration
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
Run ID: 216978bb-d16b-4477-bf79-31e524d04a99
📒 Files selected for processing (4)
NAMESPACER/converters.Rman/reexports.Rdvignettes/MSstatsMetabolomics.Rmd
1 participant
Motivation and Context
Please include relevant motivation and context of the problem along with a short summary of the solution.
Changes
Please provide a detailed bullet point list of your changes.
Testing
Please describe any unit tests you added or modified to verify your changes.
Checklist Before Requesting a Review
Motivation and Context
This change adds support for untargeted metabolomics workflows that originate in MZMine (feature quantification + spectral-library compound names) and SIRIUS (in-silico structure predictions). The solution is to (1) re-export
MZMinetoMSstatsFormatfrom theMSstatsnamespace so users can run the conversion step without separately attachingMSstatsConvert, and (2) document an end-to-end example vignette (MSstatsMetabolomics.Rmd) showing conversion, compound-level summarization, differential abundance testing, and plotting. The vignette also explains MSI Level 2 (MZMine) vs MSI Level 3 (SIRIUS) naming priorities and includes a small-fixture caveat for unreliable Lactate results.Detailed Changes
NAMESPACEMZMinetoMSstatsFormatfrom theMSstatspackage and added the correspondingimportFrom(MSstatsConvert, MZMinetoMSstatsFormat)entry.R/converters.RMZMinetoMSstatsFormatfromMSstatsConvertand re-export it via theMSstatsConvert::MZMinetoMSstatsFormatcompatibility layer.man/reexports.RdMZMinetoMSstatsFormat(new alias and cross-reference under theMSstatsConvertconverter list).vignettes/MSstatsMetabolomics.RmdMSstatsConvert)MZMinetoMSstatsFormat(..., use_log_file = FALSE)ProteinNameby priority: best MZMine compound match → SIRIUS name fallback →m/z_RTfallbackdataProcess(log2 transform, equalizeMedians normalization, TMP summarization, MBimpute enabled;use_log_file = FALSE)groupComparison(contrast.matrix = "pairwise")dataProcessPlots(ProfilePlot) andgroupComparisonPlots(VolcanoPlot aseval = FALSE)Unit Tests
tinytest-based test harness viatests/tinytest.R(tinytest::test_package("MSstats")).inst/tinytest/fixtures and test scripts (e.g.,test_dataProcess.R,test_groupComparison.R,test_groupComparisonQCPlots.R,test_making_contrasts.R, and related utils tests), along with corresponding annotation/processed-data fixtures.MZMinetoMSstatsFormat.Coding Guidelines