Function that retrieves prevalent signatures for a given tumor type/primary site Data is collected from COSMIC v3.4.

Function that retrieves prevalent signatures for a given tumor type/primary site Data is collected from COSMIC v3.4.

Usage

get_prevalent_site_signatures(
  site = "Any",
  custom_collection = NULL,
  ref_data = NULL,
  min_prevalence_pct = 0.1,
  incl_poss_artifacts = T
)

Arguments

site

Primary tumor site

custom_collection

Custom collection of signatures from COSMIC

ref_data

PCGR reference data object

min_prevalence_pct

Minimum prevalence (pct) of signature in cohorts associated with primary site - used to select reference signatures for inclusion in signature reconstruction

incl_poss_artifacts

logical indicating if artefact signatures are to be included