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Build a DBS mutational-spectrum catalog from an annotated DBS VCF

Source: R/catalog_build.R
vcf_to_dbs_catalog.Rd

Build a DBS mutational-spectrum catalog from an annotated DBS VCF

Usage

vcf_to_dbs_catalog(
  annotated_vcf,
  type = c("DBS78", "DBS136", "DBS144"),
  ref_genome = NULL,
  region = "unknown",
  sample_name = "count"
)

Arguments

annotated_vcf

A DBS 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 = "DBS144" also requires trans.strand / bothstrand.

type

One of "DBS78", "DBS136", "DBS144".

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()).