The scripts in this repository will allow you to perform the computational analyses from the paper "Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma". Be aware that external files not included in the repository are needed for all analyses. How to access the relevant files is described at the top of each script. Description of the scripts below:
functions.R - Functions needed for all scripts, source this file before running anything. preproc_celltype.R - Script for QC and assignment of cell type cna.R - Defining malignant and nonmalignant epithelial cells and division of malignant cells into subclones epithelial_analysis.R - Analysis focusing on TCGA subtypes, intertumour heterogeneity and nonmalignant epithelial cells nmf.R - Defining metaprograms through NMF hpv_analysis.R - Specific analyses to define the role of HPV in intratumour heterogeneity ext_validation.R - Validation in external datasets
Tested in R 4.1.0