gwas2crispr

GWAS-to-CRISPR: direct GWAS Catalog REST API v2 retrieval and GRCh38/hg38 CSV, BED, and optional FASTA preparation for downstream CRISPR guide-design workflows.

Overview

gwas2crispr retrieves significant genome-wide association study (GWAS) associations for an Experimental Factor Ontology (EFO) trait directly from the EMBL-EBI GWAS Catalog REST API v2.

The package prepares:

harmonised SNP metadata in CSV format
genomic intervals in BED format
optional FASTA sequences with user-defined flanking regions

All genomic outputs are prepared for GRCh38/hg38.

The package is a computational preparation workflow. It does not perform wet-lab validation, therapeutic interpretation, or biological efficacy testing.

Core functions

fetch_gwas(efo_id, p_cut = 5e-8, verbose = interactive())
run_gwas2crispr(efo_id, p_cut = 5e-8, flank_bp = 200, out_prefix = NULL, verbose = interactive())

Installation

Requirements

R >= 4.1
Direct internet access to the EMBL-EBI GWAS Catalog REST API v2
Core R packages listed in DESCRIPTION

Optional FASTA requirements

FASTA extraction requires:

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

BiocManager::install(c(
  "Biostrings",
  "GenomeInfoDb",
  "BSgenome.Hsapiens.UCSC.hg38"
))

CSV and BED outputs can still be produced without the optional FASTA packages.

Install from GitHub

if (!requireNamespace("devtools", quietly = TRUE))
  install.packages("devtools")

devtools::install_github("leopard0ly/gwas2crispr")

Quick start

library(gwas2crispr)

res <- run_gwas2crispr(
  efo_id     = "EFO_0000707",
  p_cut      = 1e-6,
  flank_bp   = 300,
  out_prefix = "lung",
  verbose    = TRUE
)

res$summary
res$written

Expected output files:

lung_snps_full.csv
lung_snps_hg38.bed
lung_snps_flank300.fa

The FASTA file is written only when the hg38 BSgenome and Biostrings packages are installed.

Thesis case-study example

library(gwas2crispr)

res <- run_gwas2crispr(
  efo_id     = "EFO_0001663",
  p_cut      = 5e-8,
  flank_bp   = 200,
  out_prefix = "prostate",
  verbose    = TRUE
)

res$summary
res$written

Object-only mode

No files are written when out_prefix = NULL.

res <- run_gwas2crispr(
  efo_id     = "EFO_0001663",
  p_cut      = 5e-8,
  flank_bp   = 200,
  out_prefix = NULL,
  verbose    = FALSE
)

res$summary
res$bed

Output files

When out_prefix is supplied, the package writes:

<prefix>_snps_full.csv
<prefix>_snps_hg38.bed
<prefix>_snps_flank<bp>.fa

Notes

Genome build is fixed to GRCh38/hg38.
GWAS retrieval uses the EMBL-EBI GWAS Catalog REST API v2 directly.
Results may change when GWAS Catalog content is updated.
Network availability and rate limits may affect retrieval.
FASTA export is optional.
CSV and BED preparation remain available without optional genome packages.
The package prepares computational outputs for downstream CRISPR guide-design workflows only.

Command-line interface

A portable script is available under:

inst/scripts/gwas2crispr.R

Example:

Rscript inst/scripts/gwas2crispr.R -e EFO_0001663 -p 5e-8 -f 200 -o prostate -v

Options:

-e, --efo — EFO trait ID, for example EFO_0001663
-p, --pthresh — p-value threshold
-f, --flank — number of flanking bases for FASTA extraction
-o, --out — output file prefix
-v, --verbose — print progress messages

Testing

devtools::test()

Network-dependent tests are skipped on CRAN.

Citation

If you use gwas2crispr, cite the Zenodo release:

https://doi.org/10.5281/zenodo.16878244

citation("gwas2crispr")

Getting help

Report issues at:

https://github.com/leopard0ly/gwas2crispr/issues