Association of rare pLoF (putative loss of function) variants with Somatic Mutational Components

Scripts to extract components via ICA & VAE, to perform network analysis and to replicate manuscript figures: The impact of rare germline variants on human somatic mutation processes.

Getting Started

• Scripts can be all run in R (at least version 3.5.0)
• Required R packages: tidyverse, dplyr, reshape2, ggplot2, wesanderson, gplots, cluster, fastICA, corrpot, ggrepel, ggrastr, ggpubr, RColorBrewer

Content

• Description of the respective scripts can be found in each sub-directory

somatic_component_extraction

• Scripts to extract somatic components via Independent Component Analysis (ICA) or Variational Autoencoder (VAE) neural network
• Variational Autoencoder in Python, recommended running in Singularity Environment (more info in /somatic_component_extraction/)

paper_figures_code

• All results from association study between rare pLoF variants and somatic components using SKAT-O are provided
• Scripts to replicate manuscript figures

network_analysis

• Scripts to perform network analysis as described in the manuscript

Interactive visualization of association results via Shiny app

https://mischanvp.shinyapps.io/rare_association_shiny/