signature_origins: signature_origins

In FunGeST/Palimpsest: Package

signature_origins

Description

Annotates each mutation in a VCF with the signature with which it is most likely associated. E.g. when Type is set to "DBS", each line in the VCF corresponding to a DBS mutation is annotated with the probility that each DBS signature caused it.

Usage

signature_origins(
  input = NULL,
  Type = Type,
  signature_contribution = signatures_exp,
  input_signatures = NULL
)

Arguments

Type	Mutation type (SBS, DBS, ID or SV).
signature_contribution	List of signatures exposure numbers and proportions matrices (output from deconvolution_fit function).
input_signatures	Matrix of the input signatures with which the VCF is to be annotated .
vcf	The input VCF file to which signature origin annotations are to be added.

Examples

vcf <- signature_origins(vcf=vcf, Type = "SBS", signature_contribution = signatures_exp, input_signatures = SBS_liver_signatures)

FunGeST/Palimpsest documentation built on June 2, 2024, 4:21 a.m.