get_mutational_vector: Get mutational vector

In jdavilal/excerno: Fillter out somatic mutations generated by the Formalin-Fixed Paraffin-Embedded (FFPE) tissue preservation technique from cancer tissue

Get mutational vector

Description

Get the mutational vector from a vcf file

Usage

get_mutational_vector(vcf.file)

get_mutational_vectors(vcf.files)

Arguments

vcf.data

The name of the vcf file

Value

A vector of mutation strings

Examples

library(MutationalPatterns)
library(tidyverse)
library(vcfR)
library(Biostrings)
library(BSgenome.Hsapiens.UCSC.hg38)

# Load file for testing
file <- system.file("extdata", "SIMULATED_SAMPLE_SBS4_1.vcf", package = "excerno")

# Load in correct output
cosmic.sigs <- get_known_signatures()
cosmic.sig4 <- as.matrix(cosmic.sigs[, 4])
ffpe.sig <- get_ffpe_signature()

sample.ffpe <- create_signature_sample_vector(ffpe.sig, 500)
sample.sig4 <- create_signature_sample_vector(cosmic.sig4, 500)

test.vector <- c(sample.ffpe, sample.sig4)
vcf.vector <- get_mutational_vector(file)

# Load files for inputing multiple vcfR objects
vcf.files <- list.files(
  system.file("extdata", package = "excerno"),
  pattern = "SIMULATED_SAMPLE_SBS4_\\d.vcf", full.names = TRUE)

sample.vectors <- get_mutational_vectors(vcf.files)

jdavilal/excerno documentation built on Aug. 27, 2022, 8:10 p.m.