Split GSVA ranks calculations, enabling distribution of computations

[rcastelo]

Split the calculation of GSVA ranks into two steps, one for row normalization and another for column rank calculation. The functions gsvaRanks() and gsvaScores() have been deprecated and replaced by gsvaRowNorm(), gsvaColRanks() and gsvaColScores(). Each of them takes two additional parameters called first and last, which allow one to restrict calculations to the range of rows (for gsvaRowNorm()) or columns (for gsvaColRanks() and gsvaColScores()) that go from first to last. By default, first=NA and last=NA to indicate no such restrictions apply. Being able to restrict calculations to a range of rows or columns, should enable distributing computations in an HPC environment across nodes with non-shared main memory. This PR closes issue #266.

[Copilot]

Pull request overview

Splits the GSVA rank calculation into separate gsvaRowNorm(), gsvaColRanks(), and gsvaColScores() methods (deprecating gsvaRanks()/gsvaScores()), each accepting first/last arguments so the row-normalization and column-rank/score stages can be distributed across HPC nodes. Supporting changes refactor the wrapData() generic and data containers to carry GSVA metadata and added assays (e.g., gsvarownr, gsvaranks), expand .check_maxmem()/.check_ondisk()/.check_sparse_load_input_expr() to honor restricted ranges, update HDF5 serialization to round-trip the new metadata, and add a details() method while reworking show(). Documentation, vignettes and unit tests are adjusted accordingly.

Changes:

• Introduce three-step API (gsvaRowNorm/gsvaColRanks/gsvaColScores) with first/last chunking and dropExistingAssays support; mark gsvaRanks/gsvaScores deprecated.
• Refactor wrapData() methods, helper checks, and .pull_param()/.gsvaParam_as_list() to embed/retrieve parameter metadata across containers and to size memory based on restricted ranges.
• Update vignettes, Rd files, tests, and HDF5 serialization helpers to use the new API and to add details() method.

Reviewed changes

Copilot reviewed 29 out of 38 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
R/gsva.R	Adds new step methods, helpers .pull_param/.gsvaParam_as_list, details(), and chunked first/last plumbing.
R/utils.R	Generalizes wrapData methods, adds range/first-last and whdim plumbing in .check_* helpers.
R/gsvaRanks_serialization.R	Reworks save/load to operate on GsvaExprData with embedded GSVA metadata.
R/GSVA-pkg-deprecated.R	Re-implements deprecated gsvaRanks/gsvaScores via new helpers.
R/ssgsea.R, R/plage.R, R/zscore.R	Updates gsva() methods to call the new .check_* and wrapData() signatures; adds details for ssgsea.
R/GsvaMethodParam.R, R/AllGenerics.R, R/AllClasses.R	Adds new generics/exports, simplified show(), details() method, updates supported classes.
R/GSVA-package.R, NAMESPACE	Adjusts imports/exports for new methods and dropped re-exports.
man/*.Rd	Regenerated docs for renamed/new methods and link fixes.
vignettes/GSVA_scRNAseq.Rmd, GSVA_proteomics.Rmd, GSVA.bib	Documents three-step API, QC workflow updates, new reference.
inst/unitTests/*	Updates tests to new API and adds chunked-range checks.
DESCRIPTION, .covrignore	Roxygen config bump and coverage exclusions for deprecated/defunct files.

Files not reviewed (9)

• man/GSVA-pkg-deprecated.Rd: Language not supported
• man/GsvaExprData-class.Rd: Language not supported
• man/GsvaMethodParam-class.Rd: Language not supported
• man/geneIdsToGeneSetCollection.Rd: Language not supported
• man/geneSets.Rd: Language not supported
• man/gsva.Rd: Language not supported
• man/gsvaAnnotation.Rd: Language not supported
• man/gsvaEnrichment.Rd: Language not supported
• man/gsvaParam-class.Rd: Language not supported

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