From 4d10a40e243b38fabcd6910344aed8f74f1be6ab Mon Sep 17 00:00:00 2001 From: Luigi Corsaro <5324491+drake69@users.noreply.github.com> Date: Tue, 16 Jun 2026 17:02:03 +0200 Subject: [PATCH 1/5] docs(NEWS): add 0.99.6 entries for PR #34 features and fixes --- NEWS.md | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) diff --git a/NEWS.md b/NEWS.md index 93abe7a..fe4c72d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,66 @@ # Changes in version 0.99.6 +## New features + +* `enrichment_CTD()` gains an `interaction_types` argument: a character + vector of CTD `InteractionActions` values (e.g. + `"increases^expression"`, `"decreases^expression"`) that filters each + chemical's gene set at enrichment time. Gene sets are rebuilt on the + fly from the new `ctd_interactions.rda` cache without re-importing; + `NULL` (default) retains full backward compatibility. Supported by all + four methods (ORA, GSEA, CAMERA, GSVA). Requires `import_CTD()` to be + re-run once to generate `ctd_interactions.rda`. + +* `enrichment_CTD()` gains a `gene_id_type` argument (`"symbol"` or + `"entrez"`) controlling whether the `EnrichedGenes` output column + reports HGNC symbols (with Entrez ID fallback for unmapped genes) or + raw Entrez IDs. Default `"symbol"` is backward compatible. + +* `enrichment_CTD(method = "ORA")` now forwards `universe`, `minGSSize`, + and `maxGSSize` to `clusterProfiler::enricher()` via `...`. Setting + `universe = de$EntrezID` restricts the background to measured genes, + avoiding inflated fold-enrichment estimates. GSEA and GSVA already + exposed `minSize`/`maxSize`; CAMERA `...` was already forwarded. + +* `import_CTD()` now caches `ctd_interactions.rda`, a long-format table + of `(ChemicalID, EntrezID, InteractionActions)` triples used by the + new `interaction_types` filter. + +* `import_CTD()` reports elapsed time, chemical count, and unique gene + count on completion. + +* `import_CTD()` detects and warns when the same `ChemicalID` appears + with multiple `ChemicalName` values (CTD data quality issue; first + name retained). Reports an informational message when the same name + is shared by multiple `ChemicalID`s (legitimate parent/derivative + pairs). + +## Bug fixes + +* Fixed `EnrichedGenes` column in GSEA output: was incorrectly set to + data frame row indices instead of gene identifiers. Gene labels are + now mapped via `AnnotationDbi::mapIds()` in `.run_gsea()`. + +* `clusterProfiler::enricher()` messages ("No gene can be mapped", + "Expected input gene ID", etc.) are now suppressed via + `suppressMessages()`. + ## Documentation +* New pkgdown article `vignettes/articles/tutorial_rnaseq_workflow.Rmd`: + a complete RNA-seq → chemical enrichment workflow using the full + GSE311566 dataset (downloaded from GEO at runtime), `limma` DE, all + four methods with recommended parameters, direction-aware GSEA, and a + per-method Dexamethasone ranking recap. + +* Vignette gains a "Gene set size filters and background universe" + section documenting `universe`, `minGSSize`/`maxGSSize` (ORA), + `minSize`/`maxSize` (GSEA, GSVA), and CAMERA's implicit minimum of 2 + genes. + +* Added a new `interaction_types` parameter description to the vignette + explaining the CTD `verb^noun` vocabulary and direction-aware analysis. + * Added a full end-to-end pipeline example at `inst/scripts/example_gse311566_full_pipeline.R`. The script downloads the complete GSE311566 Female PBMCs normalised-count From df6189516e9c11160cf2bb333c81b5dd90a6e0c3 Mon Sep 17 00:00:00 2001 From: Code Reader Date: Tue, 16 Jun 2026 17:47:38 +0200 Subject: [PATCH 2/5] review: 47 new units scanned (2026-06-16) --- .code_reader/auditor_backlog.md | 4 +- .code_reader/review_manifest.json | 3236 ++++++++++++++++------------- 2 files changed, 1808 insertions(+), 1432 deletions(-) diff --git a/.code_reader/auditor_backlog.md b/.code_reader/auditor_backlog.md index d6625af..04ea984 100644 --- a/.code_reader/auditor_backlog.md +++ b/.code_reader/auditor_backlog.md @@ -1,10 +1,10 @@ # Auditor Backlog — ctdR -Exported: 2026-06-15T17:44:31.509210 +Exported: 2026-06-16T17:24:04.329299 ## R/import_CTD.R -- **.save_ctd_cache** (function, L167-192) +- **.save_ctd_cache** (function, L245-267) [TO REVIEW] ## R/utils-input.R diff --git a/.code_reader/review_manifest.json b/.code_reader/review_manifest.json index adb178c..abb46b2 100644 --- a/.code_reader/review_manifest.json +++ b/.code_reader/review_manifest.json @@ -2,15 +2,79 @@ "project": { "name": "ctdR", "path": "/Users/lcorsaro/Documents/Progetti/RICERCA/ctdR/ctdR", - "total": 1188, - "read": 5, - "unread": 1183, - "needs_re_review": 0, - "completion_pct": 0.4, - "last_sync": "2026-06-16T11:17:28.871640", - "last_scan_commit": "1f5bedd68f946ffd085d84533430db9c7fbffc7d" + "total": 1235, + "read": 4, + "unread": 1230, + "needs_re_review": 1, + "completion_pct": 0.3, + "last_sync": "2026-06-16T17:47:38.029049", + "last_scan_commit": "65381638027be5c1b6281efb2b6a4fc721b1a02f" }, "units": [ + { + "qualified_name": ".coding_agent/2026-06-15_session.md::section::Session diary — 2026-06-15", + "file_path": ".coding_agent/2026-06-15_session.md", + "kind": "section", + "status": "unread", + "content_hash": "467c890e24a48c2c", + "notes_count": 0 + }, + { + "qualified_name": ".coding_agent/2026-06-15_session.md::section::Cosa è stato fatto", + "file_path": ".coding_agent/2026-06-15_session.md", + "kind": "section", + "status": "unread", + "content_hash": "080879b743b1f616", + "notes_count": 0 + }, + { + "qualified_name": ".coding_agent/2026-06-15_session.md::section::vignette (`ctdR.Rmd`) — ORA real-data section", + "file_path": ".coding_agent/2026-06-15_session.md", + "kind": "section", + "status": "unread", + "content_hash": "8765215682240a33", + "notes_count": 0 + }, + { + "qualified_name": ".coding_agent/2026-06-15_session.md::section::manuscript (`paper.tex` + `paper.pdf`)", + "file_path": ".coding_agent/2026-06-15_session.md", + "kind": "section", + "status": "unread", + "content_hash": "5940e35c40f61d2c", + "notes_count": 0 + }, + { + "qualified_name": ".coding_agent/2026-06-15_session.md::section::Backlog", + "file_path": ".coding_agent/2026-06-15_session.md", + "kind": "section", + "status": "unread", + "content_hash": "e1ed256a637c67a7", + "notes_count": 0 + }, + { + "qualified_name": ".coding_agent/2026-06-15_session.md::section::Decisioni prese e perché", + "file_path": ".coding_agent/2026-06-15_session.md", + "kind": "section", + "status": "unread", + "content_hash": "d44334aabc4ca789", + "notes_count": 0 + }, + { + "qualified_name": ".coding_agent/2026-06-15_session.md::section::Cosa rimane aperto", + "file_path": ".coding_agent/2026-06-15_session.md", + "kind": "section", + "status": "unread", + "content_hash": "927d245fb9f19930", + "notes_count": 0 + }, + { + "qualified_name": ".coding_agent/2026-06-15_session.md::section::Blocchi / dipendenze", + "file_path": ".coding_agent/2026-06-15_session.md", + "kind": "section", + "status": "unread", + "content_hash": "409c5bf131237691", + "notes_count": 0 + }, { "qualified_name": ".github/dependabot.yml::yaml::version", "file_path": ".github/dependabot.yml", @@ -168,7 +232,7 @@ "file_path": ".github/workflows/bioccheck.yaml", "kind": "yaml_key", "status": "unread", - "content_hash": "d4e34afac077d9f7", + "content_hash": "9de22700e24fc67f", "notes_count": 0 }, { @@ -176,7 +240,7 @@ "file_path": ".github/workflows/bioccheck.yaml", "kind": "yaml_key", "status": "unread", - "content_hash": "b176a87042fcf875", + "content_hash": "4742fc4a804ce4f8", "notes_count": 0 }, { @@ -619,6 +683,14 @@ "content_hash": "390fddfa4c775b51", "notes_count": 0 }, + { + "qualified_name": "NEWS.md::section::Changes in version 0.99.6", + "file_path": "NEWS.md", + "kind": "section", + "status": "unread", + "content_hash": "816ee97d8de26fe2", + "notes_count": 0 + }, { "qualified_name": "NEWS.md::section::Changes in version 0.99.5", "file_path": "NEWS.md", @@ -795,12 +867,28 @@ "content_hash": "fcf15295141906f9", "notes_count": 0 }, + { + "qualified_name": "R/import_CTD.R::.deduplicate_chemicals", + "file_path": "R/import_CTD.R", + "kind": "function", + "status": "unread", + "content_hash": "e7f8ec70c6cfe876", + "notes_count": 0 + }, + { + "qualified_name": "R/import_CTD.R::.map_chemical_genes", + "file_path": 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}, { "qualified_name": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js::B", "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js", @@ -9363,14 +9747,6 @@ "content_hash": "7187216412ff10e3", "notes_count": 0 }, - { - "qualified_name": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js::ae", - "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js", - "kind": "function", - "status": "unread", - "content_hash": "74f56c74b3849a34", - "notes_count": 0 - }, { "qualified_name": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js::le", "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js", From 8524497e3a71d1b1c06ba8f6182fadbbc5ee5ce5 Mon Sep 17 00:00:00 2001 From: Luigi Corsaro <5324491+drake69@users.noreply.github.com> Date: Fri, 19 Jun 2026 11:06:43 +0200 Subject: [PATCH 3/5] chore: exclude .coding_agent/ from version control --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index 42f0a4d..a8296a4 100644 --- a/.gitignore +++ b/.gitignore @@ -11,5 +11,8 @@ ctdR.Rcheck/ # .sestante/ — backlog locale, mai committato .sestante/ +# .coding_agent/ — diari di sessione AI, mai committati +.coding_agent/ + # vignette HTML è artefatto di rmarkdown::render(), non sorgente vignettes/*.html From a26eec6a07fbba36daffbdf8e0b5aa46fa05ddf0 Mon Sep 17 00:00:00 2001 From: Luigi Corsaro <5324491+drake69@users.noreply.github.com> Date: Fri, 26 Jun 2026 11:55:10 +0200 Subject: [PATCH 4/5] docs(vignettes): clarify CAMERA inputs (full expression matrix + design/contrast) CAMERA does not consume a pre-computed DEG list (unlike ORA/GSEA): it takes the full expression matrix plus design and contrast, recomputing the differential signal internally. Make the design-vs-contrast distinction explicit in both ctdR.Rmd and the RNA-seq tutorial. Refresh .code_reader auditor artifacts. --- .code_reader/auditor_backlog.md | 2 +- .code_reader/review_manifest.json | 2362 +++++++++-------- .../articles/tutorial_rnaseq_workflow.Rmd | 8 +- vignettes/ctdR.Rmd | 23 +- 4 files changed, 1312 insertions(+), 1083 deletions(-) diff --git a/.code_reader/auditor_backlog.md b/.code_reader/auditor_backlog.md index 04ea984..11e68af 100644 --- a/.code_reader/auditor_backlog.md +++ b/.code_reader/auditor_backlog.md @@ -1,6 +1,6 @@ # Auditor Backlog — ctdR -Exported: 2026-06-16T17:24:04.329299 +Exported: 2026-06-17T21:47:52.604138 ## R/import_CTD.R diff --git a/.code_reader/review_manifest.json b/.code_reader/review_manifest.json index abb46b2..6afa68a 100644 --- a/.code_reader/review_manifest.json +++ b/.code_reader/review_manifest.json @@ -2,13 +2,13 @@ "project": { "name": "ctdR", "path": "/Users/lcorsaro/Documents/Progetti/RICERCA/ctdR/ctdR", - "total": 1235, + "total": 1261, "read": 4, - "unread": 1230, + "unread": 1256, "needs_re_review": 1, 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"docs/deps/search-1.0.0/fuse.min.js::ue", "file_path": "docs/deps/search-1.0.0/fuse.min.js", "kind": "function", "status": "unread", @@ -9515,6 +9699,22 @@ "content_hash": "e7f771c0ff729021", "notes_count": 0 }, + { + "qualified_name": "docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js::ke", + "file_path": "docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js", + "kind": "function", + "status": "unread", + "content_hash": "6001f8ae3f63a25b", + "notes_count": 0 + }, + { + "qualified_name": "docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js::Se", + "file_path": "docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js", + "kind": "function", + "status": "unread", + "content_hash": "61262b501188f72d", + "notes_count": 0 + }, { "qualified_name": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js::B", "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js", @@ -9747,6 +9947,14 @@ "content_hash": "7187216412ff10e3", "notes_count": 0 }, + { + "qualified_name": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js::ae", + "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js", + "kind": "function", + "status": "unread", + "content_hash": "74f56c74b3849a34", + "notes_count": 0 + }, { "qualified_name": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js::le", "file_path": "docs/deps/jquery-3.6.0/jquery-3.6.0.min.js", diff --git a/vignettes/articles/tutorial_rnaseq_workflow.Rmd b/vignettes/articles/tutorial_rnaseq_workflow.Rmd index 814548d..87bd6cf 100644 --- a/vignettes/articles/tutorial_rnaseq_workflow.Rmd +++ b/vignettes/articles/tutorial_rnaseq_workflow.Rmd @@ -373,8 +373,12 @@ while correcting for inter-gene correlation within the gene set. It is particularly well suited to expression matrix experiments with a clear design and contrast. -We reuse the `design` matrix built for limma. `contrast = 2` selects the -`groupDex` coefficient (Dex vs DMSO). +CAMERA does not consume a pre-computed DEG result: it takes the **full +expression matrix** plus a **`design`** and a **`contrast`**, and +recomputes the differential signal internally. The chemical→gene "index" +is built by `ctdR` from CTD targets. We reuse the `design` matrix built +for limma; here `design` carries the whole layout while `contrast = 2` +selects *which* coefficient to test — the `groupDex` effect (Dex vs DMSO). ```{r camera} camera_results <- enrichment_CTD( diff --git a/vignettes/ctdR.Rmd b/vignettes/ctdR.Rmd index 610ad47..b452394 100644 --- a/vignettes/ctdR.Rmd +++ b/vignettes/ctdR.Rmd @@ -349,9 +349,26 @@ if (is_subset) { CAMERA tests, for each chemical, whether its target genes show a stronger differential signal than the rest -of the transcriptome under a user-supplied design and -contrast, while correcting for inter-gene correlation -within the gene set. Reusing the real `expr` / `grp` above: +of the transcriptome, while correcting for inter-gene +correlation within the gene set. + +Unlike ORA or GSEA, CAMERA does **not** take a pre-computed +list of differentially expressed genes. Its inputs are the +**full expression matrix** (`expr`, all genes × all samples) +together with a **`design`** matrix and a **`contrast`**: +CAMERA fits the differential model and computes the test +*internally*. The chemical-to-gene mapping (the gene-set +"index", built by `ctdR` from CTD targets intersected with +`rownames(expr)`) is handled for you. Note that `design` and +`contrast` are two distinct inputs: `design` +(e.g. `model.matrix(~ grp)`) describes the *whole* +experimental layout — intercept plus any covariates — while +`contrast` selects *which* coefficient to test (here column 2, +Dex vs DMSO). This separation lets you adjust for batch or +other nuisance covariates while keeping the test focused on a +single comparison. + +Reusing the real `expr` / `grp` above: ```{r camera} design <- model.matrix(~ grp) From 6c8181df4286cc2b3260004c4cb4506ae46a3d33 Mon Sep 17 00:00:00 2001 From: Luigi Corsaro <5324491+drake69@users.noreply.github.com> Date: Tue, 7 Jul 2026 16:36:42 +0200 Subject: [PATCH 5/5] chore(pkgdown): add Vemetric analytics snippet to site head --- _pkgdown.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/_pkgdown.yml b/_pkgdown.yml index cf756c2..d33281a 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -6,6 +6,13 @@ template: primary: "#4575B4" border-radius: 0.4rem btn-border-radius: 0.3rem + includes: + in_header: | + + home: title: ctdR — Chemical Enrichment Analysis using CTD