README.md

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

Introduction

This package is used as a classifier for determining the origin of a mutation, specifically for samples that have been preserved using formalin-fixation paraffin-embedding (FFPE). This preservation process introduces artificial FFPE-caused mutations. The new variants (mostly C to T type mutations) transform the origin mutation profile, creating difficulty in detecting the original mutation signature. Excerno quantifies the abundance of the FFPE mutational signature and uses Bayes’ formula to filter FFPE artifacts.

Excerno also includes the ability to simulate cancer samples by randomly generating mutations that corresponds to the FFPE mutational signature and a mutational signature from the Catalogue Of Somatic Mutations In Cancer.

Additional data:

• Simulated cancer samples
• The FFPE signature

Installation Guide

Dependencies

Make sure you have all of these packages installed already:

• BiocManager
• BSgenome
• ggplot2
• MutationalPatterns
• stringr
• bedr
• NMF
• BSgenome.Hsapiens.UCSC.hg38
• vcfR
• R.utils
• tidyverse

Notice that for installing some of the packages you need the BiocManager installed, for example

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")

Installing the package

install.packages("devtools")
devtools::install_github("jdavilal/excerno", dependencies = TRUE, build_vignettes = TRUE)

Resources

• Instructions on how to use the library can be found in the vignette. Also trough browseVignettes("excerno")
• The analysis, code, and figures for our paper
• Our interactive shiny app is here

Overview of package workflow

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