Use maftools to make oncoplot for silent noncoding mutations using simple customization and publicly available libraries
Download test data from:
UCSC Xenahub: (hub: https://tcga.xenahubs.net)
- Input SNV file: https://tcga-xena-hub.s3.us-east-1.amazonaws.com/download/mc3%2FBRCA_mc3.txt.gz
- Clinical data: https://tcga-xena-hub.s3.us-east-1.amazonaws.com/download/TCGA.BRCA.sampleMap%2FBRCA_clinicalMatrix
Maftools: Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 2018 Nov;28(11):1747-1756. doi: 10.1101/gr.239244.118. Epub 2018 Oct 19. PMID: 30341162; PMCID: PMC6211645.
https://bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html
Xenahub: Goldman, M.J., Craft, B., Hastie, M. et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0546-8
The data used in this example is generated by the TCGA Research Network: https://www.cancer.gov/tcga.