Analysis of contribution of SBS18 to acute myeloid leukemia, including in cases with RUNX1-RUNX1T1 fusions.
- prep_mafs.R: Read in MAF data from data sources and produce analysis-ready MAF files.
- attribution_analysis.R: Perform the main analysis.
- population_scaled_effect_per_tumor.R: Code called in main analysis to attribute cancer effects to mutational processes, as described in Cannataro et al. This script is equivalent to to the file with the same name in our cancer_causes_and_effects repository, commit 79d9aec.
- make_figure_1.R: Read in analysis outputs and create Figure 1.
- make_figure_2.R: Read in analysis outputs and create Figure 2.
- signature_stability_dotplot.R: Code called by make_figure_1.R to produce 1B dotplot.
- TCGA AML MAF data from cBioPortal under identifier laml_tcga_pan_can_atlas_2018.
- Pediatric AML MAF from Gunnarsson et al., available on request here.
- cancereffectsizeR package (installation instructions), and all other R packages used in scripts (available from CRAN or Bioconductor).