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📝 WalkthroughWalkthroughPackage version bumped to 1.17.1 with RoxygenNote updated to 7.3.3. Internal function call to Changes
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🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
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In `@DESCRIPTION`:
- Line 4: Add an explicit version bound for MSstatsPTM in the DESCRIPTION
Imports to require MSstatsPTM (>= 2.10.0) so runtime calls to groupComparisonPTM
from groupComparisonLiP that pass the new ptm_label_type and protein_label_type
parameters won't fail on older installs; update the Imports entry to include
"MSstatsPTM (>= 2.10.0)" ensuring the package dependency is enforced at install
time.
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📒 Files selected for processing (3)
DESCRIPTIONR/groupComparisonLiP.Rman/groupComparisonLiP.Rd
| Package: MSstatsLiP | ||
| Title: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments | ||
| Version: 1.17.0 | ||
| Version: 1.17.1 |
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🧩 Analysis chain
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🌐 Web query:
MSstatsPTM groupComparisonPTM function parameters ptm_label_type protein_label_type version history
💡 Result:
groupComparisonPTM() parameters: ptm_label_type, protein_label_type
ptm_label_type: labeling type for the PTM dataset; must be"LF"or"TMT"(default"LF"). [1,2]protein_label_type: labeling type for the PROTEIN (global proteome) dataset; must be"LF"or"TMT"(default"LF"). [1,2]
These parameters let MSstatsPTM run group comparisons even when the PTM and global-protein datasets use different labeling types (e.g., PTM is TMT but the proteome is label-free). [3]
Version / history (what changed, and when)
- Older MSstatsPTM (e.g., v2.0.3; Bioconductor 3.16, published 2023-04-10):
groupComparisonPTM()useddata.type(noptm_label_type/protein_label_type). [4] - Current MSstatsPTM (v2.13.0; Bioconductor 3.23, published 2026-03-03):
groupComparisonPTM()includesptm_label_typeandprotein_label_type, and notes thatdata.type“will be deprecated” in favor of the two new parameters. [1] - The planned backwards-incompatible change was announced 2025-03-19, stating
data.typewould be replaced byptm_label_type+protein_label_type, and advising for backward compatibility to set both new parameters to the olddata.typevalue. [3]
Practical migration rule: if you previously did data.type = "LF" (or "TMT"), now do ptm_label_type="LF", protein_label_type="LF" (or both "TMT"), unless you intentionally want them to differ. [1,3]
References:
[1] Bioconductor MSstatsPTM 2.13.0 PDF manual (Bioc 3.23; published 2026-03-03). (bioconductor.posit.co)
[2] MSstatsPTM reference manual (HTML) documenting allowed values for ptm_label_type / protein_label_type. (bioc.r-universe.dev)
[3] MSstats Google Group announcement (2025-03-19) describing the parameter change and rationale. (groups.google.com)
[4] Bioconductor MSstatsPTM 2.0.3 PDF manual (Bioc 3.16; published 2023-04-10). (bioconductor.statistik.uni-dortmund.de)
Citations:
- 1: https://bioconductor.posit.co/packages/3.23/bioc/manuals/MSstatsPTM/man/MSstatsPTM.pdf
- 2: https://bioc.r-universe.dev/MSstatsPTM/doc/manual.html?utm_source=openai
- 3: https://groups.google.com/g/msstats/c/Z0qrhwar4RI?utm_source=openai
- 4: https://bioconductor.statistik.uni-dortmund.de/packages/3.16/bioc/manuals/MSstatsPTM/man/MSstatsPTM.pdf
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🌐 Web query:
MSstatsPTM version 2.1 2.2 2.3 ptm_label_type protein_label_type introduced when release date
💡 Result:
When were ptm_label_type / protein_label_type introduced?
They replaced the old single data.type parameter for groupComparisonPTM() as part of the Bioconductor 3.21 cycle; MSstatsPTM 2.10.0 (Date/Publication: 2025-04-15) is documented in Bioconductor materials for that release series. [1] (The change was announced ahead of time for the “upcoming MSstats 3.21 bioconductor release”.) [2]
You can see the old interface (data.type) in MSstatsPTM 2.0.3 examples. [2]
You can see the new interface (ptm_label_type, protein_label_type) in current manuals (e.g., dataProcessPTM() and groupComparisonPTM()). [3]
Release dates for MSstatsPTM 2.1 / 2.2 / 2.3 (Bioconductor evidence)
From the Bioconductor package archives I could access:
| Version | Release date (archive timestamp / Date/Publication) | Source |
|---|---|---|
| 2.2.0 | 2023-06-26 | Bioc 3.17 archive listing [4] |
| 2.2.2 | 2023-06-28 | Bioc 3.17 archive listing [4] |
| 2.1.x | Not found in the Bioconductor archives I checked | (no Bioc archive entry located) |
| 2.3.x | Not found in the Bioconductor archives I checked | (no Bioc archive entry located) |
If you want, tell me whether you mean Bioconductor releases specifically (recommended for “release date”), or GitHub tags/releases—and I can look up whether 2.1.x / 2.3.x exist as GitHub-only versions.
🌐 Web query:
MSstatsPTM changelog release notes ptm_label_type protein_label_type
💡 Result:
-
Where this change is documented (release notes / changelog context):
- In the MSstats community announcement for the upcoming Bioconductor MSstats 3.21 release (posted Mar 19, 2025):
groupComparisonPTM()’sdata.typeparameter is being replaced by two new parameters:ptm_label_typeandprotein_label_type, to support cases where PTM and proteome data use different label types (e.g., PTM=TMT, protein=LF). Back-compat guidance: set both new parameters to the olddata.typevalue. [1]
- In the MSstats community announcement for the upcoming Bioconductor MSstats 3.21 release (posted Mar 19, 2025):
-
What the current MSstatsPTM docs say:
- In the MSstatsPTM reference manual,
groupComparisonPTM()still listsdata.typebut states it “will be deprecated in favor ofptm_label_typeandprotein_label_type”, and documents both new args as acceptingLForTMT. [2] - The manual also documents
dataProcessPTM()as takingptm_label_typeandprotein_label_typeexplicitly (same allowed values:LF/TMT). [2]
- In the MSstatsPTM reference manual,
Sources:
[1] MSstats Google Group announcement (Mar 19, 2025): “Upcoming Backwards-Incompatible Changes in MSstats 3.21 – Action Required”
[2] Bioconductor MSstatsPTM manual (PDF), sections for groupComparisonPTM and dataProcessPTM
Add MSstatsPTM (>= 2.10.0) version constraint in Imports before releasing.
groupComparisonLiP() calls groupComparisonPTM() with ptm_label_type and protein_label_type parameters, which were introduced in MSstatsPTM 2.10.0 (Bioconductor 3.21, released ~April 2025). Without a version bound, installations with older MSstatsPTM versions will fail at runtime.
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@DESCRIPTION` at line 4, Add an explicit version bound for MSstatsPTM in the
DESCRIPTION Imports to require MSstatsPTM (>= 2.10.0) so runtime calls to
groupComparisonPTM from groupComparisonLiP that pass the new ptm_label_type and
protein_label_type parameters won't fail on older installs; update the Imports
entry to include "MSstatsPTM (>= 2.10.0)" ensuring the package dependency is
enforced at install time.
1 participant
Motivation and Context
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Changes
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Testing
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Checklist Before Requesting a Review
Motivation and Context
This PR fixes a critical build issue related to how
msstatsLiPinvokes thegroupComparisonPTMfunction from the MSstatsPTM package. The previous invocation used positional arguments which could lead to parameter misalignment or compatibility issues with the upstream MSstatsPTM package. By refactoring the call to use explicit named parameters, the code becomes more maintainable and compatible with the MSstatsPTM API contract.Changes
groupComparisonPTMInvocation inR/groupComparisonLiP.R(lines 87-100):ptm_label_type = "LF"andprotein_label_type = "LF"parametersmoderated = FALSEandadj.method = "BH"parameterslog_baseparametersave_fitted_models = TRUEparameter to preserve fitted model objectspathvariable tolog_file_pathparameter for clarityuse_log_file,append,verboseR/groupComparisonLiP.R:@inheritParams MSstatsPTM::groupComparisonPTMto inherit parameter documentation from the upstream packageman/groupComparisonLiP.Rd:log_baseparameter description to specify it applies only to non-TMT experimentsgroupComparisonLiPremains unchanged; only internal implementation details were modifiedTesting
The existing comprehensive test suite in
inst/tinytest/test_groupComparisonLiP.Rvalidates the functionality:LiP.Model,TrP.Model, andAdjusted.LiP.Modelas data.tablesLiP.Model: FULL_PEPTIDE, Label, log2FC, SE, Tvalue, DF, pvalue, adj.pvalue, issue, MissingPercentage, ImputationPercentage, ProteinName, PeptideSequenceTrP.Model: Protein, Label, log2FC, SE, Tvalue, DF, pvalue, adj.pvalue, issue, MissingPercentage, ImputationPercentageAdjusted.LiP.Model: FULL_PEPTIDE, Label, log2FC, SE, Tvalue, DF, pvalue, adj.pvalue, GlobalProtein, Adjusted, ProteinName, PeptideSequence, issueCoding Guidelines
No coding guideline violations were detected. The refactoring to use named parameters is a best practice that improves code maintainability and reduces the risk of argument ordering errors when interfacing with external package functions. This change aligns with R package development best practices for calling functions with multiple parameters.