| 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:
-
associations: data frame withassociation_idandpvalue. -
risk_alleles: data frame mappingassociation_idtovariant_id.
See Also
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 |
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 |
Details
Network I/O may occur when fetching data. Only GRCh38/hg38 is supported.
Value
(Invisibly) a list with elements:
-
summary: tibble with basic counts. -
snps_full: tibble of SNP metadata. -
bed: tibble of BED intervals (if computed). -
fasta:Biostrings::DNAStringSet(if computed). -
written: character vector of file paths written (possibly empty).
See Also
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
)