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Matters Arising supplementary code

Code and source data for Glasmacher, Liu & Townsend, Matters Arising responding to Cheek et al. (Nature Genetics 2026).

Figures

Figure	Description	Script
Fig 1	Mutation rate (mu) vs. selection intensity (gamma), both ESCC stages per gene, colored by Cheek et al.'s pooled w-hat	src/01_whatif_isocontour_figure.R
Fig 2	Continuous age–selection curves for U2AF1 (AML), KRAS and BRAF V600E (CRC)	src/02_age_selection_figure.R

Reproducibility

Both figures can be reproduced entirely from the committed source data CSVs in data/. No restricted-access files are needed to regenerate the figures.

To regenerate source data from the original CESA objects (requires restricted-access files), see src/_from_restricted_cesa/README.md.

Setup

# Install renv if needed
install.packages("renv")

# Restore the package environment
renv::restore()

# Run both figures
source("src/runall.R")

Outputs are written to results/figures/.

Dependencies

R packages are managed with renv. Run renv::restore() to install all dependencies.

Data

data/derived/gene_mu_gamma_what.csv — per-gene, per-stage mutation rate (mu), selection intensity (gamma), and Cheek et al.'s pooled w-hat, used by Figure 1.

data/source_data_fig1.csv — gene-level stage-specific selection intensities and 95% CIs for ESCC (7 genes, Pre and Primary stages); despite the filename, this now feeds the companion fig3_escc plot (src/03_escc_figure.R), not Figure 1.

data/source_data_fig2_params.csv — logistic/linear age-selection model parameters and sample sizes for U2AF1 (AML), KRAS variants, and BRAF V600E (CRC).

data/source_data_fig2_ribbons.csv — pre-computed 95% CI ribbon bounds at 300 age points per variant.

Large CESA objects and restricted MAF data are not committed. See data/README.md for data provenance details.