Package {gwas2crispr}

gwas2crispr package-level imports

Description

Provides a reproducible pipeline to conduct genome-wide association studies (GWAS) and extract single-nucleotide polymorphisms (SNPs) for a human trait or disease. Given aggregated GWAS dataset(s) and a user-defined significance threshold, the package retrieves significant SNPs from the GWAS Catalog and the Experimental Factor Ontology (EFO), annotates their gene context, and can write a harmonised metadata table in comma-separated values (CSV) format, genomic intervals in the Browser Extensible Data (BED) format, and sequences in the FASTA (text-based sequence) format with user-defined flanking regions for clustered regularly interspaced short palindromic repeats (CRISPR) guide design. For details on the resources and methods see: Buniello et al. (2019) doi:10.1093/nar/gky1120; Sollis et al. (2023) doi:10.1093/nar/gkac1010; Jinek et al. (2012) doi:10.1126/science.1225829; Malone et al. (2010) doi:10.1093/bioinformatics/btq099; Experimental Factor Ontology (EFO) https://www.ebi.ac.uk/efo.

Author(s)

Maintainer: Othman S. I. Mohammed admin@leopard.ly

Other contributors:

• LEOPARD.LY LTD [copyright holder]

See Also

Useful links:

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

• Report bugs at https://github.com/leopard0ly/gwas2crispr/issues

Fetch significant GWAS associations for an EFO trait

Description

Retrieves significant GWAS Catalog associations directly from the EMBL-EBI GWAS Catalog REST API v2. The function resolves the supplied Experimental Factor Ontology (EFO) identifier to trait labels, retrieves paginated association records, filters by p-value, and returns a list used by run_gwas2crispr.

Usage

fetch_gwas(efo_id = "EFO_0001663", p_cut = 5e-08, verbose = interactive())

Arguments

Details

This function performs network calls to the GWAS Catalog REST API v2 and may be affected by service availability or rate limits.

Value

A list with:

• associations: tibble with association_id and pvalue.

• risk_alleles: tibble mapping association_id to variant_id.

• cache: internal tibble with variant metadata used downstream.

See Also

run_gwas2crispr

Examples

  a <- fetch_gwas("EFO_0000707", p_cut = 1e-6, verbose = FALSE)
  head(a$associations)

Run the GWAS-to-CRISPR export pipeline using GRCh38/hg38

Description

Runs the complete computational preparation workflow: retrieves GWAS Catalog associations through fetch_gwas, prepares SNP metadata, creates BED intervals, and optionally writes CSV, BED, and FASTA files for downstream CRISPR guide-design preparation.

Usage

run_gwas2crispr(
  efo_id,
  p_cut = 5e-08,
  flank_bp = 200,
  out_prefix = NULL,
  genome_pkg = "BSgenome.Hsapiens.UCSC.hg38",
  verbose = interactive()
)

Arguments

Details

Only GRCh38/hg38 is supported. CSV and BED outputs can be produced without genome packages. FASTA output is generated only when BSgenome.Hsapiens.UCSC.hg38 and Biostrings are installed. If FASTA dependencies are unavailable, the function still writes CSV and BED.

Value

Invisibly returns a list with:

• summary: one-row tibble with basic counts.

• chr_freq: chromosome frequency table.

• snps_full: harmonized SNP metadata.

• bed: BED-style interval table.

• fasta: DNAStringSet if FASTA was generated; otherwise NULL.

• written: character vector of written file paths.

See Also

fetch_gwas

Examples

  res <- run_gwas2crispr(
    efo_id     = "EFO_0000707",
    p_cut      = 1e-6,
    flank_bp   = 300,
    out_prefix = file.path(tempdir(), "lung"),
    verbose    = FALSE
  )
  res$summary
  res$written