{ "_id": "6a200547b401979e7344651d", "Package": "aSPU", "Version": "1.50", "Date": "2021-6-28", "Title": "Adaptive Sum of Powered Score Test", "Description": "R codes for the (adaptive) Sum of Powered Score ('SPU' and\n'aSPU') tests, inverse variance weighted Sum of Powered score\n('SPUw' and 'aSPUw') tests and gene-based and some pathway\nbased association tests (Pathway based Sum of Powered Score\ntests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test,\n'GEEaSPU' test for multiple traits - single 'SNP' (single\nnucleotide polymorphism) association in generalized estimation\nequations, 'MTaSPUs' test for multiple traits - single 'SNP'\nassociation with Genome Wide Association Studies ('GWAS')\nsummary statistics, Gene-based Association Test that uses an\nextended 'Simes' procedure ('GATES'), Hybrid Set-based Test\n('HYST') and extended version of 'GATES' test for pathway-based\nassociation testing ('GATES-Simes'). ). The tests can be used\nwith genetic and other data sets with covariates. The response\nvariable is binary or quantitative. Summary; (1) Single\ntrait-'SNP' set association with individual-level data ('aSPU',\n'aSPUw', 'aSPUr'), (2) Single trait-'SNP' set association with\nsummary statistics ('aSPUs'), (3) Single trait-pathway\nassociation with individual-level data ('aSPUpath'), (4) Single\ntrait-pathway association with summary statistics\n('aSPUsPath'), (5) Multiple traits-single 'SNP' association\nwith individual-level data ('GEEaSPU'), (6) Multiple traits-\nsingle 'SNP' association with summary statistics ('MTaSPUs'),\n(7) Multiple traits-'SNP' set association with summary\nstatistics('MTaSPUsSet'), (8) Multiple traits-pathway\nassociation with summary statistics('MTaSPUsSetPath').", "Author": "Il-Youp Kwak and others (See Author(s) in each function manual)", "Maintainer": "Il-Youp Kwak ", "VignetteBuilder": "knitr", "License": "GPL-3", "URL": "https://github.com/ikwak2/aSPU", "RoxygenNote": "7.1.0", "Repository": "https://ikwak2.r-universe.dev", "Date/Publication": "2021-06-28 16:38:24 UTC", "RemoteUrl": "https://github.com/ikwak2/aspu", "RemoteRef": "HEAD", "RemoteSha": "6d6fab02967d1b9f409426e6e9fa66e667a060de", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 10:40:31 UTC", "User": "root" }, "MD5sum": "3ccc5a761defc7b832763760f999a072", "_user": "ikwak2", "_type": "src", "_file": "aSPU_1.50.tar.gz", "_fileid": "80af33c28616c57d992897be6e702bb21bbf2a27b81a542c22111b41449f7ecf", "_filesize": 799491, "_sha256": "80af33c28616c57d992897be6e702bb21bbf2a27b81a542c22111b41449f7ecf", "_created": "2026-06-03T10:40:31.000Z", "_published": "2026-06-03T10:43:19.941Z", "_distro": "noble", "_jobs": [ { "job": 79275617888, "time": 134, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7382358285" }, { "job": 79275617916, "time": 135, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7382358778" }, { "job": 79275617866, "time": 83, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7382340229" }, { "job": 79275617874, "time": 86, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7382341570" }, { "job": 79275130184, "time": 176, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7382309786" }, { "job": 79275617856, "time": 113, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7382350514" }, { "job": 79275617957, "time": 105, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7382348062" }, { "job": 79275617953, "time": 94, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7382344001" }, { "job": 79275617862, "time": 86, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7382341382" } ], "_buildurl": "https://github.com/r-universe/ikwak2/actions/runs/26879354807", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ikwak2/aspu", "_commit": { "id": "6d6fab02967d1b9f409426e6e9fa66e667a060de", "author": "ikwak2 ", "committer": "ikwak2 ", "message": "update\n", "time": 1624898304 }, "_maintainer": { "name": "Il-Youp Kwak", "email": "ikwak2@cau.ac.kr", "login": "ikwak2", "description": "", "uuid": 944558 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "gee", "role": "Depends" }, { "package": "MASS", "role": "Depends" }, { "package": "mvtnorm", "role": "Depends" }, { "package": "fields", "role": "Depends" }, { "package": "matrixStats", "role": "Depends" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "ikwak2", "_selfowned": true, "_usedby": 1, "_updates": [], "_tags": [], "_stars": 12, "_contributors": [ { "user": "ikwak2", "count": 192, "uuid": 944558 } ], "_userbio": { "uuid": 944558, "type": "user", "name": "Il-Youp Kwak" }, "_downloads": { "count": 302, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/aSPU" }, "_mentions": 11, "_devurl": "https://github.com/ikwak2/aspu", "_searchresults": 43, "_rbuild": "4.6.0", "_assets": [ "extra/aSPU.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ikwak2/aspu", "_realowner": "ikwak2", "_cranurl": true, "_releases": [ { "version": "1.33", "date": "2015-05-27" }, { "version": "1.35", "date": "2015-06-04" }, { "version": "1.36", "date": "2015-07-28" }, { "version": "1.37", "date": "2015-08-03" }, { "version": "1.38", "date": "2015-10-26" }, { "version": "1.39", "date": "2015-12-22" }, { "version": "1.40", "date": "2016-02-18" }, { "version": "1.41", "date": "2016-03-21" }, { "version": "1.42", "date": "2016-05-02" }, { "version": "1.43", "date": "2016-09-15" }, { "version": "1.44", "date": "2016-09-22" }, { "version": "1.45", "date": "2016-10-11" }, { "version": "1.46", "date": "2016-11-08" }, { "version": "1.47", "date": "2017-05-21" }, { "version": "1.48", "date": "2017-06-24" }, { "version": "1.49", "date": "2020-05-13" }, { "version": "1.50", "date": "2021-06-28" } ], "_exports": [ "aSPU", "aSPUd", "aSPUpath", "aSPUpath2", "aSPUr", "aSPUs", "aSPUsD", "aSPUsPath", "aSPUsPath2", "aSPUw", "estcov", "GATES2", "GatesSimes", "GEEaSPU", "getlogitp", "Hyst", "minP", "MTaSPUs", "MTaSPUsSet", "MTaSPUsSetPath", "MTaSPUsSetScore", "plotPmat", "pruneSNP", "simPathAR1Snp" ], "_datasets": [ { "name": "exdat", "title": "An example data set", "object": "exdat", "file": "exdat.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "kegg9", "title": "A subset of coronary artery disease (CAD) data", "object": "kegg9", "file": "kegg9.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "SAMD11", "title": "An example data for MTaSPUsSet test", "object": "SAMD11", "file": "SAMD11.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "someGs", "title": "An example data for MTaSPUsSet test", "object": "someGs", "file": "someGs.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "aSPU", "title": "Sum of Powered Score (SPU) tests and adaptive SPU (aSPU) test for single trait - SNP set association.", "topics": [ "aSPU" ] }, { "page": "aSPUd", "title": "Adaptive Sum of powered score (SPU) tests (SPU and aSPU) based on asymptotic distribution.", "topics": [ "aSPUd" ] }, { "page": "aSPUpath", "title": "Pathway based Sum of Powered Score tests (SPUpath) and adaptive SPUpath (aSPUpath) test for single trait - pathway association.", "topics": [ "aSPUpath" ] }, { "page": "aSPUpath2", "title": "Pathway based Sum of Powered Score tests (SPUpath) and adaptive SPUpath (aSPUpath) test for single trait - pathway association. (vector version, fast when n is large)", "topics": [ "aSPUpath2" ] }, { "page": "aSPUr", "title": "Robust Sum of powered score (SPU) tests and aSPU test for a quantitative trait", "topics": [ "aSPUr" ] }, { "page": "aSPUs", "title": "Sum of Powered Score (SPUs) tests and adaptive SPU (aSPUs) test for single trait - SNP set association with GWAS summary statistics.", "topics": [ "aSPUs" ] }, { "page": "aSPUsD", "title": "Sum of Powered Score (SPUs) tests and adaptive SPU (aSPUs) test for single trait - SNP set association with GWAS summary statistics (distribution based).", "topics": [ "aSPUsD" ] }, { "page": "aSPUsPath", "title": "Pathway based Sum of Powered Score tests (SPUsPath) and adaptive SPUpath (aSPUsPath) test for single trait - pathway association with GWAS summary statistics.", "topics": [ "aSPUsPath" ] }, { "page": "aSPUsPath2", "title": "Pathway based Sum of Powered Score tests (SPUsPath) and adaptive SPUpath (aSPUsPath) test for single trait - pathway association with GWAS summary statistics. (vector version, fast when n is large)", "topics": [ "aSPUsPath2" ] }, { "page": "aSPUw", "title": "Inverse variance weighted Sum of Powered Score tests (SPUw) and adaptive SPUw (aSPUw) test for single trait - SNP set association.", "topics": [ "aSPUw" ] }, { "page": "estcov", "title": "estcov", "topics": [ "estcov" ] }, { "page": "exdat", "title": "An example data set", "topics": [ "exdat" ] }, { "page": "GATES2", "title": "Gene-based Association Test that uses an extended Simes procedure (GATES) for single trait - SNP set association", "topics": [ "GATES2" ] }, { "page": "GatesSimes", "title": "GATES-Simes test for single trait - pathway association.", "topics": [ "GatesSimes" ] }, { "page": "GEEaSPU", "title": "The SPU and aSPU tests for multiple traits - single SNP association in generalized estimating equations.", "topics": [ "GEEaSPU" ] }, { "page": "getlogitp", "title": "Get the p-values of the multiple SNPs based on the Wald test in a logistic regresion model.", "topics": [ "getlogitp" ] }, { "page": "Hyst", "title": "HYST (Hybrid Set-based Test) for single trait - pathway association", "topics": [ "Hyst" ] }, { "page": "kegg9", "title": "A subset of coronary artery disease (CAD) data", "topics": [ "kegg9" ] }, { "page": "minP", "title": "minP test.", "topics": [ "minP" ] }, { "page": "MTaSPUs", "title": "The SPU and aSPU tests for multiple traits - single SNP association with GWAS summary statistics.", "topics": [ "MTaSPUs" ] }, { "page": "MTaSPUsSet", "title": "gene-Multitrait Sum of Powered Score (MTSPUsSet) tests and adaptive MTSPUsSet (MTaSPUsSet) test for multi trait - SNP set association with GWAS summary statistics.", "topics": [ "MTaSPUsSet" ] }, { "page": "MTaSPUsSetPath", "title": "Multitraits - Pathway based Sum of Powered Score tests (MTSPUsSetPath) and adaptive MTSPUsSetpath (MTaSPUsSetPath) test for multi trait - pathway association with GWAS summary statistics.", "topics": [ "MTaSPUsSetPath" ] }, { "page": "MTaSPUsSetScore", "title": "gene-Multitrait Sum of Powered Score (MTSPUsSetScore) tests and adaptive MTSPUsSet (MTaSPUsSet) test for multi trait - SNP set association with GWAS summary statistics. (Score version added)", "topics": [ "MTaSPUsSetScore" ] }, { "page": "plotPmat", "title": "Image plot of P-value matrix.", "topics": [ "plotPmat" ] }, { "page": "pruneSNP", "title": "Prune SNPs (related to aSPUs, aSPUsPath, MTaSPUsSet)", "topics": [ "pruneSNP" ] }, { "page": "SAMD11", "title": "An example data for MTaSPUsSet test", "topics": [ "SAMD11" ] }, { "page": "simPathAR1Snp", "title": "Simulating a pathway with multiple SNPs.", "topics": [ "simPathAR1Snp" ] }, { "page": "someGs", "title": "An example data for MTaSPUsSet test", "topics": [ "someGs" ] } ], "_readme": "https://github.com/ikwak2/aspu/raw/HEAD/README.md", "_rundeps": [ "dotCall64", "fields", "gee", "maps", "MASS", "matrixStats", "mvtnorm", "RColorBrewer", "Rcpp", "spam", "viridisLite" ], "_vignettes": [ { "source": "aSPUstat.Rmd", "filename": "aSPUstat.html", "title": "Adaptive Gene- and Pathway- Trait Association testing with GWAS Summary Statistics (aSPUs() and aSPUsPath())", "engine": "knitr::rmarkdown", "headings": [ "Data", "Use of aSPUs function", "Use of aSPUsPath function" ], "created": "2015-07-24 19:41:07", "modified": "2021-06-28 15:03:00", "commits": 11 }, { "source": "MTaSPUsSet.Rmd", "filename": "MTaSPUsSet.html", "title": "Adaptive Gene - Multitrait Association testing with GWAS Summary Statistics (MTaSPUsSet() )", "author": "Il-Youp Kwak", "engine": "knitr::rmarkdown", "headings": [ "Data preparation", "Data analysis", "Data Visualization of some detected genes" ], "created": "2016-03-24 23:56:02", "modified": "2021-06-28 15:03:00", "commits": 17 } ], "_score": 7.189770956346875, "_indexed": true, "_nocasepkg": "aspu", "_universes": [ "ikwak2" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.50", "date": "2026-06-03T10:42:34.000Z", "distro": "noble", "commit": "6d6fab02967d1b9f409426e6e9fa66e667a060de", "fileid": "9143625cf681c674ff3b762a3b32e13a905de69e6c709a3b4e995fbfc7cf4970", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ikwak2/actions/runs/26879354807" }, { "r": "4.6.0", "os": "linux", "version": "1.50", "date": "2026-06-03T10:42:38.000Z", "distro": "noble", "commit": "6d6fab02967d1b9f409426e6e9fa66e667a060de", "fileid": "7bc4cfa85737463b650409152c29ec23e7537d91f259d97c7ec8cb0a66c771be", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ikwak2/actions/runs/26879354807" }, { "r": "4.5.3", "os": "mac", "version": "1.50", "date": "2026-06-03T10:41:54.000Z", "commit": "6d6fab02967d1b9f409426e6e9fa66e667a060de", "fileid": "58ac834c86a3f5b5751d1fff9cb5ab59058f5cb1d2b9e2c510ef21ba63ab143f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ikwak2/actions/runs/26879354807" }, { "r": "4.6.0", "os": "mac", "version": "1.50", "date": "2026-06-03T10:41:58.000Z", "commit": "6d6fab02967d1b9f409426e6e9fa66e667a060de", "fileid": "3e4caf7bea80148ef4b92080b26ec543c1a27326f09cfcf1dbbc494324eaa53d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ikwak2/actions/runs/26879354807" }, { "r": "4.6.0", "os": "wasm", "version": "1.50", "date": "2026-06-03T10:42:41.000Z", "commit": "6d6fab02967d1b9f409426e6e9fa66e667a060de", "fileid": "f7a7b3615bd6d4c0ca2d6c48ce601b7153e585ed17e363a221c018c0732a5c2f", "status": "success", "buildurl": "https://github.com/r-universe/ikwak2/actions/runs/26879354807" }, { "r": "4.7.0", "os": "win", "version": "1.50", "date": "2026-06-03T10:41:56.000Z", "commit": "6d6fab02967d1b9f409426e6e9fa66e667a060de", "fileid": "08156a6607124f1425e1073cd16b888de3f011f89310dbe637bd0f5ec9b31d5e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ikwak2/actions/runs/26879354807" }, { "r": "4.5.3", "os": "win", "version": "1.50", "date": "2026-06-03T10:41:45.000Z", "commit": "6d6fab02967d1b9f409426e6e9fa66e667a060de", "fileid": "a8038bc993fcbf538e36da2d2d01775563d993226894ff68d6ab0be3bce6d4c4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ikwak2/actions/runs/26879354807" }, { "r": "4.6.0", "os": "win", "version": "1.50", "date": "2026-06-03T10:41:44.000Z", "commit": "6d6fab02967d1b9f409426e6e9fa66e667a060de", "fileid": "4c66e6f1226564548c2f4dc2b150f0263c0d59af58b4589a7b2634fedc34e3ae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ikwak2/actions/runs/26879354807" } ] }