{ "_id": "6a105fb3acfb0bcc41ca66f3", "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": "2026-05-08 08:48:26 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", "MD5sum": "b39f80a3a59f1e8d76afcbdca4361785", "_user": "cran", "_type": "src", "_file": "genomicper_1.8.tar.gz", "_fileid": "eb9e0caf53e7616d2cb0924fe3f8e847cd154a0bce4067d255ac857020fc03e9", "_filesize": 235554, "_sha256": "eb9e0caf53e7616d2cb0924fe3f8e847cd154a0bce4067d255ac857020fc03e9", "_created": "2026-05-08T08:48:26.000Z", "_published": "2026-05-22T13:52:51.804Z", "_distro": "noble", "_jobs": [ { "job": 77393586577, "time": 103, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6875404734" }, { "job": 77393586603, 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{ "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", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 655, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/genomicper" }, "_mentions": 1, "_searchresults": 14, "_rbuild": "4.6.0", "_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": 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