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.
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
Data Access Tiers
| 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:
| 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
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.
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
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
Recent Changes
Recent project commits with lines added, files changed, and change categories.
Reproducibility
Session Info (click to expand)
Show code
sessionInfo()
#> R version 4.6.1 (2026-06-24)
#> Platform: x86_64-pc-linux-gnu
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#> time zone: Etc/UTC
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#> attached base packages:
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#> other attached packages:
#> [1] targets_1.12.0
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#> loaded via a namespace (and not attached):
#> [1] vctrs_0.7.3 cli_3.6.6 knitr_1.51 rlang_1.3.0
#> [5] xfun_0.60 otel_0.2.0 processx_3.9.0 jsonlite_2.0.0
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#> [41] withr_3.0.3 tools_4.6.1 secretbase_1.3.0 cachem_1.1.0