NEWS

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BreastSubtypeR 1.5.1

Bug fixes

• Fixed TNBC cohort detection in cohort-specific method selection (#133). Cohorts are now classified as TNBC only when all evaluable non-missing TN annotations indicate TN. Mixed cohorts containing both TN and nonTN samples are no longer routed to the TNBC-specific branch solely because some samples are TN.

Tests

• Added synthetic phenotype-table tests for TN-only, mixed, UNC-like mixed, and missing or partly missing TN annotations.

BreastSubtypeR 1.5.0

Highlights (from v1.1.3 onward)

• Paper published in NAR Genomics and Bioinformatics (2025), Editor's Choice (DOI: 10.1093/nargab/lqaf131).
• Support for raw RNA-seq counts (requires gene lengths).
• iBreastSubtypeR refresh: cleaner UX, smarter AUTO guidance, consistent exports.

Enhancements

• ssBC/ssBC.v2: singleton subgroup robustness: Subgroups with n=1 no longer error:
  • Keeps matrix shape (drop=FALSE) and hardens dimnames/types.
  • Primary path: original sspPredict(). Fallback: nearest-centroid (Spearman) when needed.
  • If there are 0 common PAM50 genes, returns NA labels with shaped distances/dist.RORSubtype to avoid downstream errors.
  • ROR computation guarded for incomplete inputs.
• SSPBC output now "full": BS_sspbc() and Shiny "sspbc" runs return a full metrics table (not calls-only).
  • Exports map core label columns to the standard names (Call_5class / Call_4class when applicable).
• Shiny: "Load example data..." button
  • One-click load of a small demo dataset from inst/RshinyTest/ to explore the UI without uploads.
  • Shows a notification on success; users can immediately run Preprocess & map and analyses.
• AUTO preflight UI (Shiny): Now detects cohort kind (TN, ER/HER2, ER-only, HER2-only) and shows compact stats:
  • ER/HER2 subgroups: ER+/HER2-, ER-/HER2-, ER+/HER2+, ER-/HER2+
  • TN cohorts: TN vs nonTN
  • Readiness uses the same minimums used by AUTO (sourced programmatically; no duplicated thresholds).
• Shorter notifications.
  • Routine toasts (e.g., "Step 1 complete. Proceed to Step 2.") now auto-dismiss sooner to reduce UI clutter.
• Phenodata normalization (Mapping): Accepts flexible ER/HER2/TN encodings and normalizes to canonical forms (ER+/ER-, HER2+/HER2-, TN/nonTN). Ambiguous HER2="2+" remains as-is and raises a warning.

Bug fixes

• TN cohorts + ssBC: BS_Multi() now respects TN cohorts when methods are specified manually; ssBC/ssBC.v2 switch to s = "TN" / "TN.v2" when a TN column indicates a TN cohort. Falls back to s = "ER" / "ER.v2" otherwise.
• AUTO: Fixed a crash in BS_Multi(methods = "AUTO") when ER and/or HER2 contained missing values (NA).
• AUTO internals: fixed variable name typo (samples_ERHER2.icd).
• Mapping(): Robust ENTREZID coercion (from as.character() to as.integer() with suppressed warnings).
• cIHC.itr: outList$distances now returned as numeric matrix.

Shiny

• Surface method warnings as toasts:
  • Runs are wrapped in a warning handler; package warnings (e.g., ssBC.v2 singleton fallbacks) appear as yellow notifications.
  • Warnings include subgroup, n, and example sample IDs for quick triage.
• Shiny preflight reset:
  • Fixed a stale cohort summary after switching data sources (manual uploads <-> example). The preflight panel now revalidates once inputs change.

Developer notes

• Added lightweight internal logger ._msg() and replaced scattered message() calls in AUTO to standardize package output without affecting CRAN/Bioc checks.

Documentation

• README/vignette: brief note on the example-data button and expected file locations.
• Mapping(): Column metadata clarified. Added explicit requirements for receptor fields used by AUTO and ER/HER2/TN-dependent methods (ssBC, cIHC/cIHC.itr, PCAPAM50) and for ROR covariates (TSIZE, NODE as numeric 0/1). Documented preferred coding and automatic normalization behavior.

Compatibility Notes

• SSPBC "full" output keeps previous columns for calls; additional metrics may appear.

Upgrade Notes

• Raw RNA-seq counts are supported from v1.1.3 onward (requires gene lengths).
• If you previously parsed BS / BS.Subtype, switch to Call_5class / Call_4class.
• Package API unchanged.