variant_counts: Assess variant prevalence and coverage

In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

Assess variant prevalence and coverage

Description

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.

Townsend-Lab-Yale/cancereffectsizeR documentation built on April 28, 2024, 6:14 p.m.