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Assess variant prevalence and coverage

Source: R/variant_counts.R
variant_counts.Rd

Determine variant prevalence (and how many samples have sequencing coverage) across your MAF data, or within different groups of samples.

Usage

variant_counts(cesa, variant_ids = character(), by = character())

Arguments

cesa

CESAnalysis

variant_ids

variant names ("KRAS G12C") or full variant IDs. If left empty, uses non-overlapping variants as returned by `select_variants()` with min_freq = 1.

by

Optionally, a vector of one or more sample table columns. Variant prevalence and coverage data will be broken down by the groups defined by unique combinations of values in these columns.