Add saveHDF5GSVA() / loadHDF5GSVA()#269
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… / loadHDF5GSVAranks()
…ow-normalized expression values produced by gsvaRowNorm() in the GSVA algorithm
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Pull request overview
This PR introduces new HDF5 serialization helpers for GSVA intermediate outputs, enabling save/load of both gsvaRowNorm() and gsvaColRanks() results while deprecating the older rank-only serialization API.
Changes:
- Added
saveHDF5GSVA()/loadHDF5GSVA()to serialize GSVA row-normalized and rank outputs (with metadata) via HDF5. - Deprecated
saveHDF5GSVAranks()/loadHDF5GSVAranks()and routed them through the new API. - Updated internal assay naming and documentation/tests to reflect the new serialization scope.
Reviewed changes
Copilot reviewed 8 out of 11 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| R/gsvaRanks_serialization.R | Removed the old rank-only serialization implementation (moved to deprecated wrappers). |
| R/gsva.R | Updated row-normalization assay naming and internal parameter pulling behavior. |
| R/gsva-serialization.R | Added the new generalized HDF5 save/load functions and helper to choose the GSVA assay. |
| R/GSVA-pkg-deprecated.R | Added deprecated wrappers for the previous rank-only serialization functions. |
| NAMESPACE | Exported saveHDF5GSVA() and loadHDF5GSVA(). |
| man/gsvaRanks.Rd | Updated docs to reflect the renamed row-normalized assay. |
| man/gsvaRanks_serialization.Rd | Removed the old rank-only serialization man page. |
| man/gsva-serialization.Rd | Added documentation for the new generalized serialization API. |
| man/GSVA-pkg-deprecated.Rd | Documented newly deprecated serialization wrappers. |
| inst/unitTests/test_serialization.R | Added/updated unit tests covering serialization for both row-normalized and rank outputs. |
| inst/unitTests/test_ranksserialization.R | Removed the old rank-only serialization unit tests. |
Files not reviewed (3)
- man/GSVA-pkg-deprecated.Rd: Language not supported
- man/gsva-serialization.Rd: Language not supported
- man/gsvaRanks.Rd: Language not supported
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Added two new functions
saveHDF5GSVA()andloadHDF5GSVA()that replacesaveHDF5GSVAranks()andloadHDF5GSVAranks(), and allow one to save and load the output fromgsvaColRanks()as well as fromgsvaRowNorm(). The formersaveHDF5GSVAranks()andloadHDF5GSVAranks()have been deprecated, and documentation and unit tests have been updated.