coMMpass

Reproducible analysis of the MMRF CoMMpass (Clinical Outcomes in MM to Personal Assessment of Genetic Profile) multiple myeloma study data using R and Nix.

Overview

The CoMMpass study is a landmark longitudinal genomic-clinical study of 1,143 newly diagnosed multiple myeloma patients collected between 2011-2016 with 8-year follow-up. This project provides:

Usage

Quick Start (without Nix)

# Install from GitHub (requires Bioconductor deps)
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(c("TCGAbiolinks", "DESeq2", "edgeR", "limma",
                        "SummarizedExperiment", "fgsea"))
remotes::install_github("JohnGavin/coMMpass-analysis")

# Clone the repo (targets needs _targets.R in working directory)
# git clone https://github.com/JohnGavin/coMMpass-analysis.git
# setwd("coMMpass-analysis")

# Run the pipeline
library(targets)
tar_make()

Pipeline status

The pipeline has 247 targets (total build time: 6m 59s).

Top 5 targets by build time:

name MB time
67 raw_rnaseq 60.5 1m 53s
165 deseq2_results 2.7 50s
35 clinical_data 1.2 38s
235 bayes_cox_basic 2.3 32s
164 deseq2_paired_results 2.1 26s

Example: read a result

km <- tar_read(km_overall)
str(km, max.level = 1)
#> List of 8
#>  $ n_per_group    : 994 patients
#>  $ median_survival: NA (not reached)
#>  $ fit            : survfit object
#>  $ data           : data.frame with 994 obs. of 14 variables
#>  $ formula        : survival::Surv(time_days, status) ~ 1

Note: The pipeline downloads ~3.6 GB of RNA-seq data from GDC on first run. Subsequent runs skip downloads (cue = "never"). The config target sets sample_limit = 200 by default — edit R/tar_plans/plan_data_acquisition.R to change this.

Quick Start (with Nix — fully reproducible)

# Requires Nix package manager (https://nixos.org/download.html)
chmod +x default.sh
./default.sh

# macOS only: prevent sleep during long builds
caffeinate -i ./default.sh

What Happens

  1. default.sh checks if default_dev.nix needs regeneration
  2. Runs default.R which:
    • Extracts package dependencies from DESCRIPTION (single source of truth)
    • Calls rix::rix() to generate default_dev.nix
  3. Builds the Nix environment with nix-build
  4. Creates a GC root symlink (prevents garbage collection)
  5. Enters an interactive shell with all packages

Data Access

Access Level Data Type Requirements Used by this pipeline
GDC Data Portal Clinical, RNA-seq (995 cases) None (open access) Yes
AWS Open Data RNA-seq gene expression None (AWS CLI) Yes
MMRF Researcher Gateway FISH, PFS, treatment response Free registration (pending) No (12 targets blocked)
dbGaP Controlled Raw sequences (BAM/FASTQ) Institutional IRB No

Project Structure

R/                             # Package functions & pipeline plans
R/tar_plans/                   # Modular targets plans
R/viz/                         # Visualization functions
vignettes/                     # Analysis vignettes (pkgdown articles)
inst/extdata/vignettes/        # Pre-computed RDS for CI
tests/testthat/                # Unit + snapshot tests
data/                          # Downloaded data (gitignored)
default.sh                     # Nix environment setup
default.R                      # rix configuration
README.qmd                     # README source (generates README.md)

92 R source files, 13 vignettes, 156 pre-computed RDS, 22 test files.

Key References

Glossary

See the Glossary vignette for definitions of terms used throughout this project.

Requirements

# Configure cachix caches
nix-env -iA cachix -f https://cachix.org/api/v1/install
cachix use rstats-on-nix    # Pre-built R packages
cachix use johngavin         # Compiled coMMpass R package

License

MIT