For all biomarker evidence items with specified confidence level, assign whether these are tier-defining or providing additional support - tumor-type specific query

The function considers the strength of evidence (evidence levels) and the match between biomarker site and primary site of query tumor. Mark evidence considered tier-defining, while other biomarker evidence items as additional support

Usage

assign_bm_tier_support_ttspecific(
  variants_tier_classified = NULL,
  vartype = NULL,
  primary_site = "Lung",
  etype_for_tiering = c("predictive"),
  biomarker_items = NULL
)

Arguments

variants_tier_classified

data frame with variant tier classifications based on support from biomarker evidence item

vartype

variant type (e.g. 'snv_indel', 'cna', 'fusion')

primary_site

primary tumor site of query tumor (e.g. 'Lung', 'Breast', 'Any')

etype_for_tiering

evidence type(s) to consider for tier classification

biomarker_items

data frame with biomarker evidence items

Value

data frame with biomarker evidence items classified as tier-defining or providing additional support