Calc mutation frequencies — calc_mutation_frequencies • cevomod

Calculates the CNV-corrected mutation frequencies. Implemented methods:

Dentro - calculates the Cancer Cell Fraction (CCF) using the formulas from Dentro et al. Principles of Reconstructing the Subclonal Architecture of Cancers (2015)

Usage

calc_mutation_frequencies(
  object,
  method = "Dentro",
  which_snvs = default_SNVs(object),
  which_cnvs = default_CNVs(object),
  rm_intermediate_cols = TRUE,
  verbose = get_cevomod_verbosity()
)

dentro_2015_correction(tbl)

Arguments

object: object
method: Available methods: Dentro
which_snvs: Which SNVs to use
which_cnvs: Which CNVs to use
rm_intermediate_cols: Should the columns used to get CCF be removed?
verbose: Verbose?
tbl: tibble that contains columns: VAF, total_cn, normal_cn, purity

Value

object

The same tibble with new columns: u, m, CCF (Cancer Cell Fraction)

Functions

dentro_2015_correction(): Implements the CNV-based frequency correction method described in Dentro et al. 'Principles of Reconstructing the Subclonal Architecture of Cancers' (2015)