classify_simulated_samples: Get classification of each mutation

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

Get classification of each mutation

Description

Get classification of each mutation using Bayes' Theorem.

Usage

classify_simulated_samples(samples, signatures, signature.names = c())

Arguments

samples	List of mutation samples, each coming from a different mutational signature
signatures	List of the mutational signature that each sample came from. Each element should correspond an element in argument samples at the same index.
signature.names	Vector of the signature names. Each element should correspond an element in argument signatures at the same index.

Value

A data frame with the classification of each mutation in the samples

Examples

library(MutationalPatterns)
library(tidyverse)

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

# Create samples
sample.sig4 <- create_signature_sample_vector(cosmic.sig4, 100)
sample.ffpe <- create_signature_sample_vector(ffpe.sig, 100)

samples <- list(sample.sig4, sample.ffpe)
signatures <- list(cosmic.sig4, ffpe.sig)

classify_simulated_samples(samples, signatures)
classify_simulated_samples(samples, signatures, c("SBS4", "FFPE"))

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