{ "_id": "6a19eb251d7bb097a09c7007", "Package": "RapidoPGS", "Title": "A Fast and Light Package to Compute Polygenic Risk Scores", "Version": "2.3.2", "Authors@R": "c(\nperson(\"Guillermo\",\"Reales\", role = c(\"aut\", \"cre\"), email = \"grealesm@gmail.com\", comment = c(ORCID = \"0000-0001-9993-3916\")),\nperson(\"Chris\", \"Wallace\", role = \"aut\", email = \"cew54@cam.ac.uk\", comment = c(ORCID = \"0000-0001-9755-1703\")),\nperson(\"Olly\", \"Burren\", role = \"ctb\", email = \"ob219@cam.ac.uk\", comment = c(ORCID = \"0000-0002-3388-5760\")))", "Description": "Quickly computes polygenic scores from GWAS summary\nstatistics of either case-control or quantitative traits\nwithout parameter tuning. Reales,G., Vigorito, E., Kelemen,M.,\nWallace,C. (2021) \"RápidoPGS: A\nrapid polygenic score calculator for summary GWAS data without\na test dataset\".", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make libssl-dev", "Repository": "https://grealesm.r-universe.dev", "Date/Publication": "2026-04-20 13:45:12 UTC", "RemoteUrl": "https://github.com/grealesm/rapidopgs", "RemoteRef": "HEAD", "RemoteSha": "af40a034f813e7ebf2d65780b2ea7f339053ae3a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 19:32:43 UTC", "User": "root" }, "Author": "Guillermo Reales [aut, cre] (ORCID:\n),\nChris Wallace [aut] (ORCID: ),\nOlly Burren [ctb] (ORCID: )", "Maintainer": "Guillermo Reales ", "MD5sum": "9e1cacfbaca5adb59cfbf0f9fd81708c", "_user": "grealesm", "_type": "src", "_file": "RapidoPGS_2.3.2.tar.gz", "_fileid": "4142413cc7d8c3def026a9b6076ac5b5f38601d158c60d4161d951344b5398eb", "_filesize": 3913815, "_sha256": "4142413cc7d8c3def026a9b6076ac5b5f38601d158c60d4161d951344b5398eb", "_created": "2026-05-29T19:32:43.000Z", "_published": "2026-05-29T19:38:13.191Z", "_distro": "noble", "_jobs": [ { "job": 78573055053, "time": 233, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7299450940" }, { "job": 78573055056, "time": 235, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7299451350" }, { "job": 78573055021, "time": 155, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7299430362" }, { "job": 78573055133, "time": 226, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7299464233" }, { "job": 78572377994, "time": 250, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7299374785" }, { "job": 78573054962, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78573055135, "time": 169, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7299430748" }, { "job": 78573055064, "time": 163, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7299429014" }, { "job": 78573055061, "time": 177, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7299433408" } ], "_buildurl": "https://github.com/r-universe/grealesm/actions/runs/26657786698", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/grealesm/rapidopgs", "_commit": { "id": "af40a034f813e7ebf2d65780b2ea7f339053ae3a", "author": "GRealesM ", "committer": "GRealesM ", "message": "tiny little change on thescription\n", "time": 1776692712 }, "_maintainer": { "name": "Guillermo Reales", "email": "grealesm@gmail.com", "login": "grealesm", "bluesky": "@greales7.bsky.social", "description": "Statistical geneticist and computational biologist. I love genetics, evolution, cats, coffee, and cheese bread. ", "uuid": 7490028, "orcid": "0000-0001-9993-3916" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3", "role": "Depends" }, { "package": "data.table", "role": "Depends" }, { "package": "RCurl", "role": "Depends" }, { "package": "curl", "role": "Depends" }, { "package": "magrittr", "role": "Depends" }, { "package": "dplyr", "version": ">= 1.1.3", "role": "Imports" }, { "package": "GenomicRanges", "version": ">= 1.52.0", "role": "Imports" }, { "package": "IRanges", "version": ">= 2.34.1", "role": "Imports" }, { "package": "bigsnpr", "version": ">= 1.12.2", "role": "Imports" }, { "package": "coloc", "version": ">= 5.2.3", "role": "Imports" }, { "package": "bigreadr", "version": ">= 0.2.5", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "GenomeInfoDb", "role": "Suggests" } ], "_owner": "grealesm", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-14", "n": 1 }, { "week": "2026-17", "n": 1 } ], "_tags": [ { "name": "v2.3.2", "date": "2026-04-20" } ], "_stars": 14, "_contributors": [ { "user": "grealesm", "count": 88, "uuid": 7490028 }, { "user": "chr1swallace", "count": 10, "uuid": 2189544 } ], "_userbio": { "uuid": 7490028, "type": "user", "name": "Guillermo Reales", "description": "Statistical geneticist and computational biologist. I love genetics, evolution, cats, coffee, and cheese bread. " }, "_downloads": { "count": 288, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RapidoPGS" }, "_devurl": "https://github.com/grealesm/rapidopgs", "_searchresults": 12, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/RapidoPGS.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/grealesm/rapidopgs", "_realowner": "grealesm", "_cranurl": true, "_releases": [ { "version": "1.0.2", "date": "2020-08-07" }, { "version": "2.1.0", "date": "2021-06-17" }, { "version": "2.2.0", "date": "2022-06-15" }, { "version": "2.3.0", "date": "2023-10-13" }, { "version": "2.3.1", "date": "2025-02-19" }, { "version": "2.3.2", "date": "2026-04-03" } ], "_exports": [ "create_1000G", "gwascat.download", "rapidopgs_multi", "rapidopgs_single", "sd.prior.est" ], "_datasets": [ { "name": "EUR_ld.blocks19", "title": "LD block architecture for European populations (hg19).", "object": "EUR_ld.blocks19", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "EUR_ld.blocks38", "title": "LD block architecture for European populations (hg38).", "object": "EUR_ld.blocks38", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "michailidou19", "title": "Subset of Michailidou BRCA GWAS sumstat dataset.", "object": "michailidou19", "class": [ "data.table", "data.frame" ], "fields": [ "SNPID", "CHR", "BP", "REF", "ALT", "ALT_FREQ", "BETA", "SE", "P", "N" ], "rows": 100000, "table": true, "tojson": true }, { "name": "michailidou38", "title": "Subset of Michailidou BRCA GWAS sumstat dataset.", "object": "michailidou38", "class": [ "data.table", "data.frame" ], "fields": [ "SNPID", "CHR", "BP", "REF", "ALT", "ALT_FREQ", "BETA", "SE", "P", "N" ], "rows": 100000, "table": true, "tojson": true } ], "_help": [ { "page": "create_1000G", "title": "Download 1000 Genomes Phase III panel", "topics": [ "create_1000G" ] }, { "page": "EUR_ld.blocks19", "title": "LD block architecture for European populations (hg19).", "topics": [ "EUR_ld.blocks19" ] }, { "page": "EUR_ld.blocks38", "title": "LD block architecture for European populations (hg38).", "topics": [ "EUR_ld.blocks38" ] }, { "page": "find_file_in_ftp", "title": "Finding a file in an FTP directory This is an internal function to help 'gwascat.download' find the right file", "topics": [ "find_file_in_ftp" ] }, { "page": "gwascat.download", "title": "Retrieve GWAS summary datasets from GWAS catalog ''gwascat.download' takes a PMID from the user and downloads the associated summary statistics datasets published in GWAS catalog", "topics": [ "gwascat.download" ] }, { "page": "logsum", "title": "Helper function to sum logs without loss of precision", "topics": [ "logsum" ] }, { "page": "michailidou19", "title": "Subset of Michailidou BRCA GWAS sumstat dataset.", "topics": [ "michailidou19" ] }, { "page": "michailidou38", "title": "Subset of Michailidou BRCA GWAS sumstat dataset.", "topics": [ "michailidou38" ] }, { "page": "rapidopgs_multi", "title": "Compute PGS from GWAS summary statistics using Bayesian sum of single-effect (SuSiE) linear regression using z scores", "topics": [ "rapidopgs_multi" ] }, { "page": "rapidopgs_single", "title": "Compute PGS from GWAS summary statistics using posteriors from Wakefield's approximate Bayes Factors", "topics": [ "rapidopgs_single" ] }, { "page": "sd.prior.est", "title": "Compute Standard deviation prior (SD prior) for quantitative traits using pre-computed heritability.", "topics": [ "sd.prior.est" ] }, { "page": "sdY.est", "title": "Estimate trait variance, internal function", "topics": [ "sdY.est" ] }, { "page": "wakefield_pp", "title": "compute posterior probabilities using Wakefield's approximate Bayes Factors 'wakefield_pp' computes posterior probabilities for a given SNP to be causal for a given SNP under the assumption of a single causal variant.", "topics": [ "wakefield_pp" ] }, { "page": "wakefield_pp_quant", "title": "Compute posterior probabilities using Wakefield's approximate Bayes Factors for quantitative traits", "topics": [ "wakefield_pp_quant" ] } ], "_pkglogo": "https://github.com/grealesm/rapidopgs/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/grealesm/rapidopgs/raw/HEAD/README.md", "_rundeps": [ "BH", "bigassertr", "bigparallelr", "bigreadr", "bigsnpr", "bigsparser", "bigstatsr", "bigutilsr", "BiocGenerics", "bit", "bitops", "cli", "codetools", "coloc", "cowplot", "cpp11", "crayon", "curl", "data.table", "DEoptimR", "digest", "doParallel", "doRNG", "dplyr", "farver", "ff", "flock", "foreach", "generics", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "IRanges", "irlba", "isoband", "iterators", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "matrixStats", "mixsqp", "nabor", "parallelly", "pillar", "pkgconfig", "plyr", "ps", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "reshape", "RhpcBLASctl", "rlang", "rmio", "rngtools", "robustbase", "roptim", "RSpectra", "runonce", "S4Vectors", "S7", "scales", "Seqinfo", "susieR", "tibble", "tidyselect", "triebeard", "urltools", "utf8", "vctrs", "viridis", "viridisLite", "withr" ], "_vignettes": [ { "source": "Computing_RapidoPGSmulti.Rmd", "filename": "Computing_RapidoPGSmulti.html", "title": "Computing a PGS using RápidoPGS-multi", "author": "Guillermo Reales", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation of RápidoPGS", "Setup", "Preparing reference panel", "Preparing LD matrices (UK Biobank case)", "Loading data", "Computing a PGS using RápidoPGS-multi and LD matrices", "Computing a PGS using RápidoPGS-multi and 1000 Genomes Phase III panel", "Conclusion" ], "created": "2021-04-14 17:23:40", "modified": "2026-03-30 16:49:50", "commits": 8 }, { "source": "Computing_RapidoPGSsingle.Rmd", "filename": "Computing_RapidoPGSsingle.html", "title": "Computing a PGS using RápidoPGS-single and GWAS catalog", "author": "Guillermo Reales", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation of RápidoPGS", "Setup", "Downloading data from GWAS catalog", "Applying quality control to the dataset", "Computing PGS using RápidoPGS-single", "Applying different thresholds", "Conclusion" ], "created": "2021-04-14 17:23:40", "modified": "2026-03-30 16:49:50", "commits": 5 } ], "_score": 5.5263392773898445, "_indexed": true, "_nocasepkg": "rapidopgs", "_universes": [ "grealesm" ], "_binaries": [ { "r": "4.5.1", "os": "wasm", "version": "2.3.2", "date": "2026-04-03T07:29:13.000Z", "commit": "a2261e291de53e34b8e95efd9ac52422c99031d5", "fileid": "21edcee1ee14ca33be8d496afc28c0891f8e51f5c68f2562a101b7328f0a2382", "status": "success", "buildurl": "https://github.com/r-universe/grealesm/actions/runs/23938020724" }, { "r": "4.7.0", "os": "linux", "version": "2.3.2", "date": "2026-05-29T19:35:40.000Z", "distro": "noble", "commit": "af40a034f813e7ebf2d65780b2ea7f339053ae3a", "fileid": "0e03ec823be0cec888297892b3e4931bfdf4a2005d69596a0683d3cde6e7480d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/grealesm/actions/runs/26657786698" }, { "r": "4.6.0", "os": "linux", "version": "2.3.2", "date": "2026-05-29T19:35:44.000Z", "distro": "noble", "commit": "af40a034f813e7ebf2d65780b2ea7f339053ae3a", "fileid": "20929c96433c8467fa3d654a244c00be33e842abb4332fe0b173b0875772d249", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/grealesm/actions/runs/26657786698" }, { "r": "4.5.3", "os": "mac", "version": "2.3.2", "date": "2026-05-29T19:34:56.000Z", "commit": "af40a034f813e7ebf2d65780b2ea7f339053ae3a", "fileid": "f83f620902aba61de34d62bc039f628886c1b2dfa30a5887292a05d3fb7b6ac4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/grealesm/actions/runs/26657786698" }, { "r": "4.6.0", "os": "mac", "version": "2.3.2", "date": "2026-05-29T19:36:11.000Z", "commit": "af40a034f813e7ebf2d65780b2ea7f339053ae3a", "fileid": "38b295bb450c6d98c469d76d226ab9831903eac563af497d3d64275d358d043d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/grealesm/actions/runs/26657786698" }, { "r": "4.7.0", "os": "win", "version": "2.3.2", "date": "2026-05-29T19:34:34.000Z", "commit": "af40a034f813e7ebf2d65780b2ea7f339053ae3a", "fileid": "7072d9df6c9baa88aa46f5b3e298a206ab30a5c352e51fd65374ca7d0cbaad35", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/grealesm/actions/runs/26657786698" }, { "r": "4.5.3", "os": "win", "version": "2.3.2", "date": "2026-05-29T19:34:32.000Z", "commit": "af40a034f813e7ebf2d65780b2ea7f339053ae3a", "fileid": "ae1de6dd7e42fdd1e086459e862c809a079c606bdce987ad0c3a1b1eca865d2c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/grealesm/actions/runs/26657786698" }, { "r": "4.6.0", "os": "win", "version": "2.3.2", "date": "2026-05-29T19:34:39.000Z", "commit": "af40a034f813e7ebf2d65780b2ea7f339053ae3a", "fileid": "8acaa63903ab3891a86ca44bd6ff8f1cf5191d44a7f0e44474b02d0e6db70544", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/grealesm/actions/runs/26657786698" } ] }