R code for the RNAseq data analysis

1. Run the code in Rcode

2. Using the data in the reference folder if needed

3. Example rendered PDF files are in the output folder

Read depth ratio plot and BAF plot for the multi-region samples

1. Tumor copy number data (Read depth ratio) and BAF data was generated by GATK somatic copy number vairant discovery pipeline:https://gatk.broadinstitute.org/hc/en-us/articles/360035535892-Somatic-copy-number-variant-discovery-CNVs-

2. RD and BAF plot was generated by Hatchet software: https://github.com/raphael-group/hatchet