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Build an SBS mutational-spectrum catalog from an annotated SBS VCF

Source: R/catalog_build.R
vcf_to_sbs_catalog.Rd

Returns a single catalog matrix of the requested type. Intermediate matrices for the other SBS resolutions are still computed (cheap) but not returned, keeping the public API focused on "one call, one catalog type".

Usage

vcf_to_sbs_catalog(
  annotated_vcf,
  type = c("SBS96", "SBS192", "SBS1536"),
  ref_genome = NULL,
  region = "unknown",
  sample_name = "count"
)

Arguments

annotated_vcf

An SBS VCF annotated by annotate_sbs_or_dbs_vcf(). May be the bare annotated data.table or the full list(annotated.vcf, discarded.variants) returned by the annotator. Must contain a seq.<N>bases column; for type = "SBS192" also requires trans.strand / bothstrand.

type

One of "SBS96", "SBS192", "SBS1536".

ref_genome

Optional BSgenome object or alias; recorded on the output catalog.

region

One of "genome", "exome", "transcript", "unknown".

sample_name

Column name for the single-sample catalog matrix.

Value

A single-column numeric matrix with catalog attributes (see as_catalog()).