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MsVariants: validated variant calls with somaticness provenance

Source: R/classes-variants.R
MsVariants.Rd

An [MsVariants] object holds a canonical variant table plus the genome build and the somaticness signal provenance. It is the input container for [ms_catalog()] and the tally step. Channel/label matching everywhere in msuiter is by label, never by position.

Usage

MsVariants(table = NULL, genome = character(0), provenance = list())

Arguments

table

data.frame with the canonical variant columns.

genome

single non-empty string naming the genome build.

provenance

named list with the somaticness signal fields.

Details

Required columns of `table`: `chrom`, `start`, `end`, `ref`, `alt`. Optional columns: `vaf` (numeric in [0, 1]) and `filter` (character, FILTER confidence passthrough). Coordinates are 1-based and closed (`start >= 1`, `end >= start`); alleles are uppercase `A/C/G/T/N`.

Required `provenance` fields: `caller` (non-empty character) and `matched_normal` (single character, `"none"` for tumor-only calls). Optional field: `vaf_floor` (numeric in [0, 1]).