Integrates clonality input to help prioritize neoantigens downstream.

garnish_clonality(dt)

Arguments

dt

Data table. Passed internally from garnish_affinity, requires allelic_fraction or cellular_fraction columns.

Value

A data table with added clonality columns:

  • clone_id: rank of the clone containing the variant (highest equals larger tumor fraction).

  • cl_proportion: estimated mean tumor fraction containing the clone.