{ "_id": "6a4ca2f407c3fd5c3260ebe2", "Package": "genomicper", "Type": "Package", "Title": "Circular Genomic Permutation using Genome Wide Association\np-Values", "Version": "1.8", "Date": "2026-02-21", "Authors@R": "c(person(given = c(\"Claudia\", \"P\"),\nfamily = \"Cabrera\",\nrole = c(\"aut\", \"cre\"),\nemail = \"c.cabrera@qmul.ac.uk\"),\nperson(given = \"Pau\",\nfamily = \"Navarro\",\nrole = \"aut\"),\nperson(given = c(\"Chris\", \"S\"),\nfamily = \"Haley\",\nrole = \"aut\"))", "Maintainer": "Claudia P Cabrera ", "Description": "Circular genomic permutation approach uses genome wide\nassociation studies (GWAS) results to establish the\nsignificance of pathway/gene-set associations whilst accounting\nfor genomic structure. All single nucleotide polymorphisms\n(SNPs) in the GWAS are placed in a 'circular genome' according\nto their location. Then the complete set of SNP association\np-values are permuted by rotation with respect to the SNPs'\ngenomic locations. Two testing frameworks are available:\npermutations at the gene level, and permutations at the SNP\nlevel. The permutation at the gene level uses Fisher's\ncombination test to calculate a single gene p-value, followed\nby the hypergeometric test. The SNP count methodology maps each\nSNP to pathways/gene-sets and calculates the proportion of SNPs\nfor the real and the permutated datasets above a pre-defined\nthreshold. Genomicper requires a matrix of GWAS association\np-values and SNPs annotation to genes. Pathways can be obtained\nfrom within the package or can be provided by the user. Cabrera\net al (2012) .", "License": "GPL-2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-07 06:53:30 UTC", "User": "root" }, "Author": "Claudia P Cabrera [aut, cre], Pau Navarro [aut], Chris S Haley\n[aut]", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-02-23 16:10:17 UTC", "RemoteUrl": "https://github.com/cran/genomicper", "RemoteRef": "HEAD", "RemoteSha": "a870ab42a3741aea2457c60bc58ad5cf748fe9df", "_user": "cran", "_type": "src", "_file": "genomicper_1.8.tar.gz", "_fileid": "https://r2.ropensci.org/7a94b8350751b0bc29d3a2e74fbcf773066e60296e17ab9399a13b2b4df6d217", "_filesize": 235812, "_sha256": "7a94b8350751b0bc29d3a2e74fbcf773066e60296e17ab9399a13b2b4df6d217", "_expires": "2026-10-15T06:55:47.000Z", "_created": "2026-07-07T06:53:30.000Z", "_published": "2026-07-07T06:55:48.835Z", "_jobs": [ { "job": 85554692679, "time": 100, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8130181641" }, { "job": 85554692683, "time": 100, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8130182218" }, { "job": 85554387101, "time": 120, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8130150701" }, { "job": 85554692660, "time": 76, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8130174716" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/cran/actions/runs/28847383767", "_status": "success", "_upstream": "https://github.com/cran/genomicper", "_commit": { "id": "a870ab42a3741aea2457c60bc58ad5cf748fe9df", "author": "Claudia P Cabrera ", "committer": "cran-robot ", "message": "version 1.8\n", "time": 1771863017 }, "_maintainer": { "name": "Claudia P Cabrera", "email": "c.cabrera@qmul.ac.uk" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "graphics", "role": "Imports" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-09", "n": 1 } ], "_tags": [ { "name": "1.8", "date": "2026-02-23" } ], "_stars": 1, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 617, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 629, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/genomicper" }, "_mentions": 1, "_searchresults": 14, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/genomicper.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.3", "date": "2012-05-29" }, { "version": "1.6", "date": "2016-07-05" }, { "version": "1.7", "date": "2021-05-08" }, { "version": "1.8", "date": "2026-02-23" } ], "_exports": [ "genes_permutation", "genome_order", "get_results", "hyprbg", "plot_results", "read_pvals", "read2_paths", "snps_permutation" ], "_datasets": [ { "name": "demo", "title": "GWAS p_values demo data", "object": "demo", "file": "demo.rda", "class": [ "data.frame" ], "fields": [ "name", "Trait1", "Trait2", "Trait3", "Trait4", "Trait5", "Trait6", "Trait7", "Trait8", "Trait9" ], "rows": 1000, "table": true, "tojson": true }, { "name": "RHSA109582", "title": "Reactome Pathway examples", "object": "RHSA109582", "file": "RHSA109582.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "RHSA1474244", "title": "Reactome Pathway examples", "object": "RHSA1474244", "file": "RHSA1474244.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "RHSA164843", "title": "Reactome Pathway examples", "object": "RHSA164843", "file": "RHSA164843.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "RHSA446343", "title": "Reactome Pathway examples", "object": "RHSA446343", "file": "RHSA446343.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "RHSA8876384", "title": "Reactome Pathway examples", "object": "RHSA8876384", "file": "RHSA8876384.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "RHSA8964572", "title": "Reactome Pathway examples", "object": "RHSA8964572", "file": "RHSA8964572.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "SNPsAnnotation", "title": "SNPs-Genes annotation to Distance 0 (SNPs within a gene)", "object": "SNPsAnnotation", "file": "SNPsAnnotation.rda", "class": [ "data.frame" ], "fields": [ "name", "Chromosome", "Location", "GENE_ID", "Symbol", "Orientation" ], "rows": 1007, "table": true, "tojson": true } ], "_help": [ { "page": "genomicper-package", "title": "Circular Genomic Permutations", "topics": [ "genomicper-package", "genomicper" ] }, { "page": "demo", "title": "GWAS p_values demo data", "topics": [ "demo" ] }, { "page": "genes_permutation", "title": "Gene-level Permutations", "topics": [ "genes_permutation" ] }, { "page": "genome_order", "title": "Genome Order", "topics": [ "genome_order" ] }, { "page": "get_results", "title": "Circular Permutation Results", "topics": [ "get_results" ] }, { "page": "hyprbg", "title": "Hypergeometric Test (phyper)", "topics": [ "hyprbg" ] }, { "page": "plot_results", "title": "Plot Results Circular Permutation", "topics": [ "plot_results" ] }, { "page": "read_pvals", "title": "Read GWAS p-values of association and Merge with SNP annotations", "topics": [ "read_pvals" ] }, { "page": "read2_paths", "title": "Read to SNPs to sets; Map SNPs to gene-sets/pathways", "topics": [ "read2_paths" ] }, { "page": "RHSAXXXXX", "title": "Reactome Pathway examples", "topics": [ "RHSA109582", "RHSA1474244", "RHSA164843", "RHSA446343", "RHSA8876384", "RHSA8964572", "RHSAXXXXX" ] }, { "page": "snps_permutation", "title": "SNP-level permutations", "topics": [ "snps_permutation" ] }, { "page": "SNPsAnnotation", "title": "SNPs-Genes annotation to Distance 0 (SNPs within a gene)", "topics": [ "SNPsAnnotation" ] } ], "_rundeps": [], "_score": 1.146128035678238, "_indexed": true, "_nocasepkg": "genomicper", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.8", "date": "2026-07-07T06:55:10.000Z", "distro": "resolute", "commit": "a870ab42a3741aea2457c60bc58ad5cf748fe9df", "fileid": "https://r2.ropensci.org/66931cde321bcc2ebc296ac99f4c5ce97c82380d65af95d119bcdb1a3cc63326", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28847383767" }, { "r": "4.6.1", "os": "linux", "version": "1.8", "date": "2026-07-07T06:55:13.000Z", "distro": "resolute", "commit": "a870ab42a3741aea2457c60bc58ad5cf748fe9df", "fileid": "https://r2.ropensci.org/362a67b5b4c99a2e076d2cd34699d8968609234d340cb18ebe80b5f73007cd1a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/28847383767" }, { "r": "4.6.0", "os": "wasm", "version": "1.8", "date": "2026-07-07T06:55:00.000Z", "commit": "a870ab42a3741aea2457c60bc58ad5cf748fe9df", "fileid": "https://r2.ropensci.org/d3f2ed9ddbdc4891a6f1d653aa625985eb883c9dba92488804eba26e2120e78b", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/28847383767" } ] }