Spatial association between transposable elements and clinically significant variants (hg38)

MSc Bioinformatics dissertation, University of Edinburgh, 2025-26.

Overview

A computational pipeline testing the spatial association between transposable elements (TEs) and common, pathogenic and benign single-nucleotide variants (SNVs) in the human genome (GRCh38/hg38). Association is assessed by permutation-based overlap testing (regioneR) and by SNV-density comparison against intergenic and coding-sequence backgrounds, together with a CpG-deamination signature analysis.

Repository structure

b293325_bioinf/
├── README.md
├── R/                     # helper functions sourced by the analyses
│   └── functions.R
├── bash_scripts/          # data retrieval (run first)
│   ├── get_dbsnps.sh
│   ├── get_snp_common.sh
│   ├── get_tes.sh
│   └── get_cpg.sh
├── analysis/              # R Markdown analyses
│   ├── cpg_alu_overlaps.Rmd
│   ├── te_snp_overlap.Rmd
│   └── te_snp_common_density.Rmd
├── data/                  # inputs; populated by the scripts in bash_scripts/ (not tracked)
└── figures/               # outputs; written by knitting the analyses (not tracked)

Environment

R 4.5.1, Bioconductor 3.22. Each analysis ends with a call to sessionInfo(), so the exact package versions are printed in the knitted output of every Rmd; a consolidated copy is also given in Appendix A of the dissertation. Key packages: GenomicRanges, regioneR, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg38(.masked), TxDb.Hsapiens.UCSC.hg38.knownGene, ggplot2, here.

How to run

1. Retrieve the input data (from a shell, in the project root):

   bash bash_scripts/get_dbsnps.sh      # clinical SNVs (dbSNP, via EDirect)
   bash bash_scripts/get_snp_common.sh  # common SNVs (UCSC dbSnp155Common)
   bash bash_scripts/get_tes.sh         # TE annotations (UCSC RepeatMasker)
   bash bash_scripts/get_cpg.sh         # CpG islands (UCSC), for the positive control

   These write their outputs into data/.

2. Run the analyses by knitting the R Markdown files (in this order):

   File	Produces
   analysis/cpg_alu_overlaps.Rmd	Figure 2 (positive control)
   analysis/te_snp_overlap.Rmd	[Figures 4, 8, 9]
   analysis/te_snp_common_density.Rmd	[Figures 3, 5, 6, 7]

   Figures are written to figures/. R/functions.R is sourced by the analyses and is not run directly.

Notes on reproducibility

• File paths are resolved with the here package relative to the project root, so clone the repository and run from the top-level folder (or open it as the working directory). Do not run scripts from inside the subfolders.
• The data/ and figures/ folders are intentionally empty in the repository; they are populated by step 1 and step 2 respectively. Raw inputs are public and re-downloadable, so they are regenerated rather than stored here.