Type: Package
Title: GWAS-to-CRISPR Data Pipeline for High-Throughput SNP Target Extraction
Version: 0.1.2
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.
License: MIT + file LICENSE
URL: https://github.com/leopard0ly/gwas2crispr
BugReports: https://github.com/leopard0ly/gwas2crispr/issues
Depends: R (≥ 4.1)
Imports: httr, dplyr, purrr, tibble, tidyr, readr, methods
Suggests: gwasrapidd, Biostrings, BSgenome.Hsapiens.UCSC.hg38, optparse, testthat, knitr, rmarkdown
VignetteBuilder: knitr, rmarkdown
Encoding: UTF-8
Language: en-US
RoxygenNote: 7.3.2
biocViews: Software, Genetics, VariantAnnotation, SNP, DataImport
NeedsCompilation: no
Packaged: 2025-08-19 14:14:00 UTC; hp
Author: Othman S. I. Mohammed [aut, cre], LEOPARD.LY LTD [cph]
Maintainer: Othman S. I. Mohammed <admin@leopard.ly>
Repository: CRAN
Date/Publication: 2025-08-22 18:50:06 UTC

Fetch significant GWAS associations for an EFO trait

Description

Tries gwasrapidd::get_associations() first; if it returns no rows or fails, falls back to the EBI GWAS Summary Statistics REST API to retrieve significant associations up to the given p-value threshold.

Usage

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

Arguments

efo_id

character. Experimental Factor Ontology (EFO) trait identifier (e.g., "EFO_0001663").

p_cut

numeric. P-value threshold for significance (default 5e-8).

Details

This function performs network calls and may be rate-limited. Column names returned by the REST API may change; defensive checks are applied.

Value

An S4 object of class "associations" with slots:

See Also

run_gwas2crispr

Examples


  # Network call; may be rate-limited, so we mark it as \donttest.
  a <- try(fetch_gwas("EFO_0001663", p_cut = 5e-8), silent = TRUE)
  if (!inherits(a, "try-error")) {
    head(a@associations)
  }

Run the GWAS to CRISPR export pipeline (hg38)

Description

End-to-end pipeline: fetch significant associations, annotate, and optionally write CSV/BED/FASTA outputs. By default no files are written; set out_prefix to write results.

Usage

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

Arguments

efo_id

character. Experimental Factor Ontology (EFO) identifier, e.g., "EFO_0001663".

p_cut

numeric. P-value threshold for significance (default 5e-8).

flank_bp

integer. Flanking bases for FASTA sequences (default 200).

out_prefix

character or NULL. File prefix (including path) for outputs. If NULL (default), nothing is written to disk and a result object is returned. To write files safely in examples/tests, use file.path(tempdir(), "prefix").

genome_pkg

character. BSgenome package to use for FASTA (default "BSgenome.Hsapiens.UCSC.hg38"); FASTA step is skipped if not installed.

verbose

logical. If TRUE, emit progress via message().

Details

Network I/O may occur when fetching data. Only GRCh38/hg38 is supported.

Value

(Invisibly) a list with elements:

See Also

fetch_gwas

Examples


  # Write into a temporary directory so we don't touch the user's filespace:
  tmp <- tempdir()
  res <- run_gwas2crispr(
    efo_id     = "EFO_0001663",
    p_cut      = 5e-8,
    flank_bp   = 200,
    out_prefix = file.path(tmp, "prostate"),
    verbose    = FALSE
  )

  # If you omit 'out_prefix', nothing is written; an object is returned:
  res2 <- run_gwas2crispr(
    efo_id     = "EFO_0001663",
    p_cut      = 5e-8,
    flank_bp   = 200,
    out_prefix = NULL,
    verbose    = FALSE
  )