write_classification_to_vcf: Write classification data frame to VCF file

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

Write classification data frame to VCF file

Description

Add probabilities from classification data frame to a VCF file

Usage

write_classification_to_vcf(file, classifications.df)

Arguments

file	An VCF file
classification.df	Classification data frame with mutations as a column and posteriors for signatures. Must have 96 rows.

Examples

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

vcf.file <- system.file("extdata", "SIMULATED_SAMPLE_SBS4_1.vcf", package = "excerno")

# Load in signatures
cosmic.sigs <- get_known_signatures()

# Get signatures
signatures <- matrix(nrow = 96, ncol = 2)
signatures[,1] <- cosmic.sigs[,4]
signatures[,2] <- get_ffpe_signature()
rownames(signatures) <- get_mutation_types()
colnames(signatures) <- c("SBS4", "FFPE")

# Get contributions
contribution <- matrix(nrow = 2, ncol = 1)
contribution[,1] <- c(0.5, 0.5)
rownames(contribution) <- c("SBS4", "FFPE")

classification.df <- get_classification(signatures, contribution)
write_classification_to_vcf(vcf.file, classification.df)

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