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Build an ID (indel) mutational-spectrum catalog from an annotated ID VCF

Source: R/catalog_build.R
vcf_to_id_catalog.Rd

Turns an indel-annotated VCF (with COSMIC_83 / Koh_89 / Koh_476 columns as produced by annotate_id_vcf()) into a count matrix for the requested ID classification scheme.

Usage

vcf_to_id_catalog(
  annotated_vcf,
  type = c("ID83", "ID89", "ID476"),
  ref_genome = NULL,
  region = "unknown",
  sample_name = "count",
  FILTER_PASS = TRUE,
  clip_le_9 = TRUE
)

Arguments

annotated_vcf

An ID VCF annotated by annotate_id_vcf(). May be the bare annotated data.table or the full list(annotated.vcf, discarded.variants) returned by the annotator. Must contain the categorization column corresponding to type.

type

One of "ID83", "ID89", "ID476".

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.

FILTER_PASS

If TRUE, retain only rows where the VCF FILTER column is "PASS".

clip_le_9

If TRUE, drop variants with repeat count R > 9, approximating PCAWG indel calling.

Value

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