Data Sources & Provenance

Overview

This vignette documents all data sources used in the coMMpass analysis pipeline, their access tiers, and the distinction between pipeline data (real patient data from GDC) and synthetic test data (generated by example_data()).

MMRF CoMMpass Study

The Multiple Myeloma Research Foundation (MMRF) Relating Clinical Outcomes in Multiple Myeloma to Personal Assessment of Genetic Profile (CoMMpass) study is a longitudinal observational study of ~1,143 newly diagnosed multiple myeloma patients.

ClinicalTrials.gov: NCT01454297
GDC Project: MMRF-COMMPASS
MMRF Researcher Gateway: https://research.themmrf.org/ (not currently accessible — FISH, PFS, treatment response data unavailable)
dbGaP Controlled Access: phs000748 (not used by this pipeline — requires institutional IRB)

Citation

Keats JJ, et al. Interim Analysis Of The Mmrf CoMMpass Trial, a Longitudinal Study In Multiple Myeloma Relating Clinical Outcomes to Genomic and Immunophenotypic Profiles. Blood. 2013;122(21):532. doi:10.1182/blood.V122.21.532.532

Data at a Glance

Summary of all datasets used by the coMMpass pipeline. Rows = records (patients/samples/treatment lines). Columns = variables per record. All data sourced from GDC open-access endpoints; MMRF Gateway data (FISH, PFS, response) not yet available.
Dataset	Rows	Columns	Completeness	Source
Clinical metadata	995	88	ISS: 100%	GDC API (open)
Treatment records	7184	5	994 patients	GDC API (open)
RNA-seq (STAR counts)	100	60660	100%	GDC STAR-Counts
MSigDB gene sets	708	2	Hallmark + KEGG	Pre-bundled parquet

Data Access Tiers

Tier	Data	Access	Used by pipeline
Open Access	RNA-seq counts (STAR), clinical metadata, treatment records	GDC Data Portal, no login required	Yes
Open Access (S3)	RNA-seq files	`s3://gdc-mmrf-commpass-phs000748-2-open/`	Yes
MMRF Gateway	FISH/cytogenetics, PFS, treatment response	Free registration (pending access)	No — 12 targets blocked
Controlled Access	WGS, WES, protected clinical	dbGaP application (phs000748)	No — requires institutional IRB

Pipeline Data Sources (Real)

The targets pipeline downloads real patient data from GDC:

Data	Source	Function
RNA-seq SummarizedExperiment	GDC STAR-Counts	`download_rnaseq_data()` via `TCGAbiolinks::GDCdownload()`
Clinical metadata (demographics, ISS, vital status)	GDC clinical endpoint	`download_clinical_data()` via `TCGAbiolinks::GDCquery_clinic()`
Treatment records (7,184 records, 994 patients)	GDC API	`download_clinical_data()` via GDC REST API
Biospecimen metadata	GDC biospecimen endpoint	`download_clinical_data()` via `TCGAbiolinks::GDCquery_clinic()`
MSigDB gene sets (Hallmark + KEGG)	MSigDB	Pre-bundled parquet in `inst/extdata/msigdb/`

The pipeline runs with a configurable sample_limit parameter (default 200 in local builds; CI uses 20). All vignettes load pre-computed results from the targets store.

GDC Documentation

GDC Data Portal: https://portal.gdc.cancer.gov/
GDC API: https://api.gdc.cancer.gov/
GDC Data Dictionary: https://docs.gdc.cancer.gov/Data_Dictionary/viewer/
mRNA Analysis Pipeline: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/

Synthetic Test Data (`example_data()`)

The example_data() function returns small synthetic datasets for testing and documentation examples. These are randomly generated with set.seed(42) and contain no real patient data.

Dataset	Size	Description
`rnaseq_se`	50 genes x 20 samples	SummarizedExperiment with simulated counts
`clinical`	20 patients	Simulated demographics and outcomes
`cytogenetic`	20 patients	Simulated FISH markers and risk groups
`treatment`	~40 rows	Simulated treatment lines (1-3 per patient)

Stored in inst/extdata/example/*.rds and created by create_all_example_data().

The two data tracks do not mix: pipeline vignettes use real GDC data via tar_read(); unit tests and ?example_data examples use synthetic data only.

MSigDB Gene Sets

Pre-bundled MSigDB Hallmark gene sets are stored as parquet files in inst/extdata/msigdb/. These are public reference gene sets used for pathway enrichment analysis.

Bundled Files

MSigDB gene set collections bundled in inst/extdata/msigdb/ (2 parquet files). Total: 708 gene sets across 4,393 unique Ensembl gene IDs. Gene_Sets = distinct pathways per collection; Unique_Genes = genes annotated in that collection. Source: MSigDB Hallmark + KEGG via msigdbr. See differential-expression GSEA/ORA sections for enrichment results.
File	Size	Rows	Columns	Gene_Sets	Unique_Genes	ID_Type
hallmark_ensembl.parquet	41.8 KB	7333	2	50	4393	Ensembl
kegg_ensembl.parquet	43 KB	9688	2	658	2795	Ensembl

Citation

Liberzon A, et al. The Molecular Signatures Database (MSigDB) Hallmark Gene Set Collection. Cell Systems. 2015;1(6):417-425. doi:10.1016/j.cels.2015.12.004

MSigDB: https://www.gsea-msigdb.org/gsea/msigdb/
R package: msigdbr

Recent Changes

Recent project commits with lines added, files changed, and change categories.

Last 20 project commits with change statistics. Date = commit date; Type = conventional-commit prefix (feat/fix/docs/ci/refactor/test/chore). Files = number of files modified; +Lines/-Lines = lines added/removed. Source: git log –numstat. See changes-by-type table for aggregate breakdown.
date	type	summary	n_files	lines_added	lines_removed	file_categories
2026-03-14	Bug Fix	fix(pipeline): Fix 11 NULL targets — DE condition, ID matching, consensus type	41	146	47	Other, R Source
2026-03-14	Bug Fix	fix(cachix): Remove –watch-mode auto flag (already default)	1	1	1	Other
2026-03-14	Bug Fix	fix(pipeline): Fix 3 NULL-target bugs, auto-generate package.nix (#93)	87	235	80	Config, Docs, Other, R Source
2026-03-14	Bug Fix	fix(nix): Fix cachix signing key, rebuild Bioconductor-dependent targets	2	0	0	Other
2026-03-14	New Feature	feat(captions): Add dynamic captions to 34 table/plot targets	22	579	89	Other, R Source
2026-03-14	Bug Fix	fix(vignettes): Enforce zero-computation rule — 22 violations → 0	32	360	764	Other, R Source, Vignettes
2026-03-13	Bug Fix	fix(vignettes): Convert kable RDS to data.frames, fix telemetry eval guards	18	8	2	Other, Vignettes
2026-03-13	Bug Fix	fix(ci): Save data frames (not DT widgets) to RDS for Nix portability	3	0	0	Other
2026-03-13	Bug Fix	fix(vignettes): Use Quarto #\| eval syntax for pkgdown-banner chunks	11	44	11	Vignettes
2026-03-13	Refactoring	refactor(targets): Move Bioconductor packages to per-target declarations	11	35	17	Other, R Source, Vignettes
2026-03-13	New Feature	feat(vignettes): Add code provenance, kable→DT conversion, caption compliance	35	1004	437	CI/CD, Other, R Source, Vignettes
2026-03-13	Bug Fix	fix(vignettes): Skip NULL RDS in safe_tar_read, return invisible(NULL)	11	22	22	Vignettes
2026-03-13	Bug Fix	fix(glossary): Prevent double DT::datatable() wrapping in glossary-table chunk	1	3	1	Vignettes
2026-03-13	CI/CD	ci: Show quarto errors with quiet=FALSE, render individual vignettes in diagnostic	1	20	6	CI/CD
2026-03-13	CI/CD	ci: Add verbose quarto error diagnostics on build failure	1	14	1	CI/CD
2026-03-13	Bug Fix	fix(vignettes): Strip Nix paths from DT widgets, auto-wrap data frames	25	66	28	CI/CD, Other, Vignettes
2026-03-13	CI/CD	ci: Add diagnostic quarto render step to debug build failure	1	17	0	CI/CD
2026-03-13	Bug Fix	fix(vignettes): Revert safe_tar_read placeholder, guard gene-report	11	12	56	Vignettes
2026-03-13	Maintenance	chore: Export vig_count_distribution_plot as ggplot RDS (513KB)	1	0	0	Other
2026-03-13	Bug Fix	fix(vignettes): Enable code eval in CI with RDS fallback	80	113	74	CI/CD, Other, R Source, Vignettes

Reproducibility

Session Info (click to expand)

Show code

sessionInfo()
#> R version 4.5.3 (2026-03-11)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.3 LTS
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#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
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#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
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#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
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#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
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#>  [1] vctrs_0.7.2         cli_3.6.5           knitr_1.51         
#>  [4] rlang_1.1.7         xfun_0.57           otel_0.2.0         
#>  [7] processx_3.8.6      targets_1.12.0      jsonlite_2.0.0     
#> [10] data.table_1.18.2.1 glue_1.8.0          prettyunits_1.2.0  
#> [13] backports_1.5.0     htmltools_0.5.9     ps_1.9.1           
#> [16] rmarkdown_2.30      tibble_3.3.1        evaluate_1.0.5     
#> [19] base64url_1.4       fastmap_1.2.0       yaml_2.3.12        
#> [22] lifecycle_1.0.5     compiler_4.5.3      codetools_0.2-20   
#> [25] igraph_2.2.2        pkgconfig_2.0.3     digest_0.6.39      
#> [28] R6_2.6.1            tidyselect_1.2.1    pillar_1.11.1      
#> [31] callr_3.7.6         magrittr_2.0.4      withr_3.0.2        
#> [34] tools_4.5.3         secretbase_1.2.0

Overview

MMRF CoMMpass Study

Citation

Data at a Glance

Data Access Tiers

Pipeline Data Sources (Real)

GDC Documentation

Synthetic Test Data (example_data())

MSigDB Gene Sets

Bundled Files

Citation

Recent Changes

Reproducibility

Synthetic Test Data (`example_data()`)