Restore Bioconductor-compatible QScore APIs

[drighelli]

Summary

This restores the published QScore API contract while retaining the revised QScore implementation introduced by PRs #64 and #65.

• adds canonical computeQScore(), computeQScoreFlags(), computeOutliersQScore(), and applyQScoreModel()
• retains deprecated QCScore entry points and their historical output and metadata names
• restores plotting and getModelFormula() argument compatibility
• restores public computeLambda(trainDF, modelFormula) and moves matrix-based work to an internal helper
• preserves valid user formulas exactly, including supported subsets and selected interactions
• derives training-label metrics from the supported base predictors in a custom formula
• validates the supported predictor whitelist and technology-specific border term
• preserves model-transfer matrix column order and legacy transfer outputs
• updates documentation, NEWS, tests, and the devel version to 1.1.9

Custom formula training labels

For a custom modelFormula, its supported base QC metrics now determine outlier computation, good/bad training-cell selection, and QScore_train, as well as the fitted model. Interactions do not add training metrics. In the CosMx border expression, log2AspectRatio is the training metric and dist_border remains an auxiliary variable.

The default modelFormula=NULL workflow, 0.1% outlier threshold, and intercept policy are unchanged.

Compatibility details

Supported formula predictors are log2SignalDensity, Area_um, log2AspectRatio, and log2Ctrl_total_ratio. The CosMx-only border expression remains technology-gated.

The intercept policy is intentionally unchanged and remains a follow-up item.

Validation

• targeted modelFormula tests: passed
• targeted QCScores tests: passed
• complete devtools::test() suite: passed
• all four vignettes rendered successfully against the checkout
• R CMD build --no-build-vignettes: passed for version 1.1.9
• BiocCheck::BiocCheckGitClone(): 0 errors, 0 warnings, 0 notes
• full devtools::check(), R CMD check, and install-dependent tarball BiocCheck are blocked because the local machine has R 4.5.1 while the package correctly declares R >= 4.6.0 for current Bioconductor devel
• before that final metadata requirement was applied, R CMD check passed examples, tests, vignettes, and the PDF manual, with one environmental dependency patch-version warning

Versioning

Version 1.1.9 assumes this branch is squash-merged. If commits are imported individually into the Bioconductor devel repository, the z component should instead be advanced per imported commit.