fix(MSstats+): Fix download analysis code#209
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📝 WalkthroughWalkthroughThe PR adds optional anomaly-score processing in Spectronaut conversion (run-order loading and anomaly parameters) and makes MSstats protein summarization method configurable; it also conditionally appends an AnomalyScores quality-metrics plot when enabled. ChangesAnomaly-score integration across data conversion and preprocessing
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Actionable comments posted: 2
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Inline comments:
In `@R/utils.R`:
- Around line 980-987: The else branch building the codes string uses hardcoded
SpectronauttoMSstatsFormat parameters (filter_with_Qvalue = TRUE, qvalue_cutoff
= 0.01, removeProtein_with1Feature = TRUE and fewMeasurements="remove") which
diverges from the if-branch and from getData() runtime behavior that use
input$q_val, input$q_cutoff, input$remove and do not include fewMeasurements;
update the else branch that appends to codes so it uses the same input variables
(input$q_val, input$q_cutoff, input$remove) and remove or align the
fewMeasurements argument to match the converter_args used in getData() and the
if branch, ensuring SpectronauttoMSstatsFormat invocations are consistent across
both branches.
- Around line 966-978: The anomalyModelFeatures vector passed into
SpectronauttoMSstatsFormat uses column names that violate MSstats+ requirements
(they start with "F." and include spaces/dots), so update the entries in
anomalyModelFeatures inside the call to SpectronauttoMSstatsFormat to use the
exact precursor-level column names present in your Spectronaut output and that
conform to MSstats+ naming (e.g., remove leading "F.", remove dots/spaces and
match parentheses style like FGShapeQualityScore(MS2) if that is the real
column), or replace them with other valid precursor-level feature column names;
verify the exact column names in your input data and ensure anomalyModelFeatures
contains those exact strings before calling SpectronauttoMSstatsFormat.
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Motivation and Context
This PR fixes generation of the R code users download from MSstatsShiny so it correctly supports Spectronaut anomaly-score computation and makes the protein summarization method configurable. Generated reproducible code now conditionally includes anomaly-score processing (loading run-order, anomaly-model parameters, parallel/core settings) when enabled, and uses the UI-selected summarization method instead of a hardcoded "TMP".
Detailed Changes
R/utils.R — getDataCode()
filetype == 'spec') the generated conversion call to SpectronauttoMSstatsFormat() is now conditional oncalculate_anomaly_scores:run_order_path.R/utils.R — preprocessDataCode()
qc_input$summaryMethodwith fallback to"TMP"instead of being hardcoded.loadpage_input$calculate_anomaly_scoresis true, appended generated plotting code callsMSstats::MSstatsQualityMetricsPlot()for metric = "AnomalyScores" withisPlotly = TRUE.No exported function signatures were changed.
Unit Tests
calculateAnomalyScores = TRUE.runOrderreference/path is present.anomalyModelFeaturesvector is present.n_trees(100) is present.Coding Guidelines Observations