Genome interpreter

[nicola-calonaci]

Generate summary results object with the following features:

• Sample-wise information:

  • Driver mutations with selection score
  • Mutation rate
  • Clone-tree structure
    • CCF for each clone
    • Number of mutations for each clone
  • Exposure distribution of each clone to signatures
    • SparseSignatures:: sigAssignmentLasso() (https://rdrr.io/bioc/SparseSignatures/man/sigAssignmentLasso.html) using subclones as individual samples

• Mutation-wise information:

  • Karyotype
  • Assignment to single-sample cluster
  • Assignment to multi-sample cluster
  • Assignment to mutational signature
  • Selection score (dnds fashion)

• Patient-wise information:

  • Sample tree (phylogeny)
  • Muller plot object