dot-variant_counts: Internal variant prevalence and coverage calculation
In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

.variant_counts

R Documentation

Internal variant prevalence and coverage calculation

Called by variant_counts() (and select_variants()) with validated inputs.

.variant_counts(
  cesa,
  samples,
  snv_from_aac,
  noncoding_snv_id,
  by_cols = character()
)

`cesa`	CESAnalysis
`samples`	validated samples table
`snv_from_aac`	data.table with columns aac_id, snv_id (validated and with annotations in CESAnalysis)
`noncoding_snv_id`	vector of snv_ids to treat as noncoding variants
`by_cols`	validated column names from sample table that are suitable to use for counting by.