excerno_vcf: Exercerno VCF

In popopo19/excerno: Fillter out somatic mutations generated by the Formalin-Fixed Paraffin-Embedded (FFPE) tissue preservation technique from cancer tissue

Exercerno VCF

Description

excerno_vcf() produces filtered vcf files. It uses NMF or nonnegative linear combination of mutation signatures to determine contribution of signatures in samples. Then Bayes' Theroem is used to classify each variant.

Usage

excerno_vcf(files, method = "nmf", num.signatures = 2, target.sigs = c())

Arguments

files	VCF files
method	A string. The method used to determine the signatures (if not given) and calculate the contributions of each signature
num.signatures	Number of signatures. Necessary arugment for when method "linear" is choosen.
target.sig	Matrix of the target signatures.Necessary arugment for when method "linear" is choosen.

Value

Object containing the vcf objects and classification data frame

Examples

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

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

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

# Using nmf
excerno_vcf(files)
excerno_vcf(files, num.signatures = 3)

# Using linear method

target.sigs <- matrix(nrow = 96, ncol = 2)
target.sigs[,1] <- cosmic.sig4
target.sigs[,2] <- ffpe.sig
rownames(target.sigs) <- get_mutation_types()
colnames(target.sigs) <- c("SBS4", "FFPE")

excerno_vcf(files, "linear", 2, target.sigs)

popopo19/excerno documentation built on Aug. 28, 2022, 1:23 a.m.