SparseSignatures: An R package using LASSO-regularized non-negative matrix factorization to identify mutational signatures from human tumor samples

Abstract

Summary: We outline the features of the R package SparseSignatures and its application to determine the signatures contributing to mutation profiles of tumor samples. We describe installation details and illustrate a step-by-step approach to (1) prepare the data for signature analysis, (2) determine the optimal parameters, and (3) employ them to determine the signatures and related exposure levels in the point mutation dataset.For complete details on the use and execution of this protocol, please refer to Lal et al. (2021). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Bioinformatics
• Cancer
• Genomics