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Assign tiers of clinical significance (AMP/ASCO/CAP framework) to somatic CNAs

Source: R/variant_classification.R
assign_variant_tiers_cna.Rd

Function that assigns tiers of clinical significance (AMP/ASCO/CAP framework) to somatic CNAs based on biomarker evidence items. The function considers the strength of evidence (evidence levels) and the match between biomarker site and primary site of query tumor. The function also considers gene properties - oncogenes and tumor suppressor genes - which are used to assign tier 3 status to variants with uncertain clinical significance.

Usage

assign_variant_tiers_cna(
  primary_site = "Any",
  biomarker_mapping_confidence = "medium",
  var_df = NULL,
  etype_for_tiering = c("predictive"),
  biomarker_items = NULL
)

Arguments

primary_site

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

biomarker_mapping_confidence

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

var_df

data frame with somatic CNAs

etype_for_tiering

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

biomarker_items

data frame with biomarker evidence items

Value

data frame with tier classifications for somatic CNAs based on biomarker evidence items and variant properties