Function that gathers data tables on diagnostic variants

Usage

prep_diagn_display_tbl(
  rep = NULL,
  tier = c(1, 2),
  etype_for_tiering = c("diagnostic"),
  clnsig = "diagnostic_positive",
  tier_defining_eitems_only = TRUE,
  variant_category = "snv_indel"
)

Arguments

rep: report object
tier: tier level(s) to consider for display (e.g. 1, 2)
etype_for_tiering: evidence type(s) to consider for tiering (e.g. 'diagnostic')
clnsig: clinical significance to consider for tiering (e.g. 'diagnostic_positive', 'diagnostic_negative')
tier_defining_eitems_only: consider only evidence items that were used for tiering (e.g. for tier 1: only evidence items with A-level evidence, for tier 2: only evidence items with B-level evidence). If FALSE, all evidence items associated with each variant, not only the tier-defining evidence items, will be considered for display in the report.
variant_category: cna, snv_indel, or fusion