Analyses associated with

Cannataro et al. APOBEC mutagenesis and selection for NFE2L2 contribute to the origin of lung squamous-cell carcinoma

published in the journal Lung Cancer here: https://www.lungcancerjournal.info/article/S0169-5002(22)00544-X/fulltext

To reproduce the calculations within the manuscript, you need to download the raw data from their free open sources. They should be stored within this directory as called within input_data/LUSC_data_combine_ms.R

1. Download TCGA.LUSC.mutect.95258183-63ea-4c97-ae29-1bae9ed06334.DR-10.0.somatic.maf.gz from https://portal.gdc.cancer.gov/files/95258183-63ea-4c97-ae29-1bae9ed06334
2. Download 18-0439R1 SuppTables 1and3_081318.xlsx from https://academic.oup.com/jnci/article/110/11/1171/5144449#supplementary-data
3. Download the sequencing data associated with this manuscript from https://doi.org/10.7303/syn31770233

Then you may run the analysis by

1. Running input_data/LUSC_data_combine_ms.R
2. Running LUSC_APOBEC_NFE2L2_analysis.Rmd