{ "_id": "6adc6a071f8fc22f6383df8f", "Package": "SIP", "Type": "Package", "Title": "Single-Iteration Permutation for Large-Scale Biobank Data", "Version": "0.1.0", "Authors@R": "c(person(\"Aubrey\", \"Annis\", role = c(\"aut\", \"cre\"), email = \"acannis@umich.edu\"))", "Description": "A single, phenome-wide permutation of large-scale biobank\ndata. When a large number of phenotypes are analyzed in\nparallel, a single permutation across all phenotypes followed\nby genetic association analyses of the permuted data enables\nestimation of false discovery rates (FDRs) across the phenome.\nThese FDR estimates provide a significance criterion for\ninterpreting genetic associations in a biobank context. For the\nbasic permutation of unrelated samples, this package takes a\nsample-by-variable file with ID, genotypic covariates,\nphenotypic covariates, and phenotypes as input. For data with\nrelated samples, it also takes a file with sample pair-wise\nidentity-by-descent information. The function outputs a\npermuted sample-by-variable file ready for genome-wide\nassociation analysis. See Annis et al. (2021)\n for details.", "URL": "https://github.com/acannis/SIP", "BugReports": "https://github.com/acannis/SIP/issues", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "Repository": "https://acannis.r-universe.dev", "Date/Publication": "2026-06-26 21:52:24 UTC", "RemoteUrl": "https://github.com/acannis/sip", "RemoteRef": "HEAD", "RemoteSha": "434de59a11d602d83f1394b492fa7dd8926e3833", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-24 08:14:44 UTC", "User": "root" }, "Author": "Aubrey Annis [aut, cre]", "Maintainer": "Aubrey Annis ", "_user": "acannis", "_type": "src", "_file": "SIP_0.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/7b81f51191e7bedf0d1ad889c2b5232e86f6f6e9ea293c14611d809b1af85bf0", "_filesize": 1608956, "_sha256": "7b81f51191e7bedf0d1ad889c2b5232e86f6f6e9ea293c14611d809b1af85bf0", "_expires": "2027-02-01T08:19:17.000Z", "_created": "2026-10-24T08:14:44.000Z", "_published": "2026-10-24T08:19:19.033Z", "_upstream": "https://github.com/acannis/sip", "_status": "success", "_maintainer": { "name": "Aubrey Annis", "email": "acannis@umich.edu", "login": "acannis", "description": "", "uuid": 31316212 }, "_jobs": [ { "job": 120823309611, "time": 125, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12553294566" }, { "job": 120823309672, "time": 119, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12553767458" }, { "job": 120823309660, "time": 219, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "12553916771" }, { "job": 120823309714, "time": 170, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "12552889478" }, { "job": 120822759032, "time": 165, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12553074844" }, { "job": 120823309702, "time": 100, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12553537421" }, { "job": 120823309671, "time": 66, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12553841279" }, { "job": 120823309669, "time": 75, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "12553688102" }, { "job": 120823309713, "time": 80, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12553592201" } ], "_buildurl": "https://github.com/r-universe/acannis/actions/runs/40077097218", "_commit": { "id": "434de59a11d602d83f1394b492fa7dd8926e3833", "author": "acannis <31316212+acannis@users.noreply.github.com>", "committer": "GitHub ", "message": "Update sip.R", "time": 1782510744 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "acannis", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-43", "n": 3 }, { "week": "2025-45", "n": 2 }, { "week": "2026-26", "n": 12 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "acannis", "count": 21, "uuid": 31316212 }, { "user": "mkleinsa", "count": 13, "uuid": 39565600 } ], "_userbio": { "uuid": 31316212, "type": "user", "name": "acannis", "followers": 0 }, "_downloads": { "count": 232, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SIP" }, "_devurl": "https://github.com/acannis/sip", "_searchresults": 1, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "extra/SIP.html", "LICENSE" ], "_homeurl": "https://github.com/acannis/sip", "_realowner": "acannis", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2025-12-11" } ], "_exports": [ "phenotype_IBD_correlation", "plot_phenotype_correlations", "sip", "sip_pair" ], "_datasets": [ { "name": "sip_exampleData", "title": "Single-iteration permutation phenotype and covariate data", "object": "sip_exampleData", "class": [ "data.table", "data.frame" ], "fields": [], "rows": 10000, "table": true, "tojson": true }, { "name": "sipPair_exampleData", "title": "Single-iteration paired permutation phenotype and covariate data", "object": "sipPair_exampleData", "class": [ "data.table", "data.frame" ], "fields": [], "rows": 10000, "table": true, "tojson": true }, { "name": "sipPair_relatednessData", "title": "Single-iteration paired permutation relatedness data", "object": "sipPair_relatednessData", "class": [ "data.table", "data.frame" ], "fields": [ "IID1", "IID2", "PropIBD" ], "rows": 9886, "table": true, "tojson": true } ], "_help": [ { "page": "get_fixed", "title": "This function subsets the sample-by-variable dataframe to the \"fixed\" (i.e., non-permuted) data. This subset should include ID variables, sex, and genotypic covariates.", "topics": [ "get_fixed" ] }, { "page": "get_pairPerm", "title": "This function samples individuals by pairs for permuting phenotype vectors in the paired-permutation function (sipPair.R)", "topics": [ "get_pairPerm" ] }, { "page": "get_pairPermDF", "title": "This function recombines the fixed data and permuted data in the paired-permutation function (sipPair.R) into a permuted sample-by-variable data frame.", "topics": [ "get_pairPermDF" ] }, { "page": "get_permDF", "title": "This function recombines the fixed data and permuted data into a permuted sample-by-variable data frame.", "topics": [ "get_permDF" ] }, { "page": "get_permIdx", "title": "This function samples indices for permuting phenotype vectors in the basic permutation function (sip.R) and for permuting leftover unpaired individuals in the paired-permutation function (sipPair.R).", "topics": [ "get_permIdx" ] }, { "page": "get_permute", "title": "This function subsets the sample-by-variable data frame to the permutable data. This subset should include phenotypes and phenotypic covariates.", "topics": [ "get_permute" ] }, { "page": "get_relCat", "title": "This function infers relatedness categories in the paired-permutation function (sip_pair.R) prior to permutation.", "topics": [ "get_relCat" ] }, { "page": "get_relPairs", "title": "This function pairs individuals in the paired-permutation function (sip_pair.R) into the most highly-related pairs possible.", "topics": [ "get_relPairs" ] }, { "page": "get_sexDF", "title": "This function divides the sample-by-variable data frame into males and females prior to permutation within sexes.", "topics": [ "get_sexDF" ] }, { "page": "get_singSamp", "title": "This function checks for uneven numbers of individuals within relatedness category and creates a data set for permuting single samples that will not be pair permuted (sip_pair.R).", "topics": [ "get_singSamp" ] }, { "page": "order_permDF", "title": "This function reorders the permuted sample-by-variable data frame to match the ID order of the primary sample-by-variable data frame.", "topics": [ "order_permDF" ] }, { "page": "phenotype_IBD_correlation", "title": "Phenotype-IBD correlation", "topics": [ "phenotype_IBD_correlation" ] }, { "page": "plot_phenotype_correlations", "title": "Phenotype correlation plot", "topics": [ "plot_phenotype_correlations" ] }, { "page": "sip", "title": "Single-iteration permutation for large-scale biobank data", "topics": [ "sip" ] }, { "page": "sip_exampleData", "title": "Single-iteration permutation phenotype and covariate data", "topics": [ "sip_exampleData" ] }, { "page": "sip_pair", "title": "Single-iteration paired permutation for large-scale biobank data with relatedness", "topics": [ "sip_pair" ] }, { "page": "sipPair_exampleData", "title": "Single-iteration paired permutation phenotype and covariate data", "topics": [ "sipPair_exampleData" ] }, { "page": "sipPair_relatednessData", "title": "Single-iteration paired permutation relatedness data", 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