Assign top tiers of clinical significance (AMP/ASCO/CAP framework) to variants based on data from biomarker evidence items (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.

Usage

assign_variant_top_tiers_ttspecific(
  biomarker_items = NULL,
  biomarker_mapping_confidence = "high",
  var_df = NULL,
  etype_for_tiering = c("predictive"),
  primary_site = "Lung"
)

Arguments

biomarker_items

data frame with biomarker evidence items

biomarker_mapping_confidence

confidence level of variant-biomarker mapping resolution (e.g. 'high' or 'medium')

var_df

data frame with variants (SNVs/InDels, CNAs, fusions)

etype_for_tiering

evidence type(s) to consider for tier classification (e.g. 'predictive', 'prognostic', 'diagnostic')

primary_site

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

Value

data frame with top tier classifications for variants based on biomarker evidence items