{ "_id": "6ae999f99ceaa78f2009c7c8", "Package": "chopsticks", "Title": "The 'snp.matrix' and 'X.snp.matrix' Classes", "Version": "1.79.0", "Date": "2018-02-05", "Author": "Hin-Tak Leung ", "Description": "Implements classes and methods for large-scale SNP\nassociation studies", "Maintainer": "Hin-Tak Leung ", "License": "GPL-3", "URL": "http://outmodedbonsai.sourceforge.net/", "Collate": "ld.with.R ss.R contingency.table.R glm_test.R ibs.stats.R\nindata.R ld.snp.R ld.with.R.eml.R misc.R outdata.R qq_chisq.R\nread.chiamo.R read.HapMap.R read.snps.pedfile.R single.R\nstructure.R wtccc.sample.list.R wtccc.signals.R xstuff.R zzz.R", "LazyLoad": "yes", "biocViews": "Microarray, SNPsAndGeneticVariability, SNP,\nGeneticVariability", "NeedsCompilation": "yes", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:35:07 UTC", "RemoteUrl": "https://github.com/bioc/chopsticks", "RemoteRef": "HEAD", "RemoteSha": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "Packaged": { "Date": "2026-11-01 13:24:27 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "chopsticks_1.79.0.tar.gz", "_fileid": "https://r2.ropensci.org/513747c72e575e03dc4c53eb659348a221d7414054f4a8aac9939eddb8889061", "_filesize": 7148494, "_sha256": "513747c72e575e03dc4c53eb659348a221d7414054f4a8aac9939eddb8889061", "_expires": "2027-02-09T15:47:09.000Z", "_created": "2026-11-01T13:24:27.000Z", "_published": "2026-11-03T08:23:21.265Z", "_upstream": "https://github.com/bioc/chopsticks", "_status": "success", "_maintainer": { "name": "Hin-Tak Leung", "email": "htl10@users.sourceforge.net", "login": "hintak", "description": "", "uuid": 14662953 }, "_jobs": [ { "job": 125802767939, "time": 132, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13214572653" }, { "job": 125802770693, "time": 140, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "13085655873" }, { "job": 125802769710, "time": 209, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "13085704274" }, { "job": 125802769783, "time": 117, "config": "linux-release-arm64", "r": "4.6.2", "check": "WARNING", "artifact": "13086080226" }, { "job": 125802770771, "time": 197, "config": "linux-release-x86_64", "r": "4.6.2", "check": "WARNING", "artifact": "13085744125" }, { "job": 125802768348, "time": 77, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 125802770161, "time": 154, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "13089793417" }, { "job": 125802771152, "time": 137, "config": "macos-release-arm64", "r": "4.6.2", "check": "WARNING", "artifact": "13089851798" }, { "job": 125802770490, "time": 349, "config": "macos-release-x86_64", "r": "4.6.2", "check": "WARNING", "artifact": "13089803691" }, { "job": 125802769646, "time": 609, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13085746090" }, { "job": 125802770760, "time": 93, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13086880284" }, { "job": 125802770655, "time": 279, "config": "windows-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "13085821646" }, { "job": 125802769972, "time": 141, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "13086206751" }, { "job": 125802771338, "time": 109, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "13085921218" }, { "job": 125802769687, "time": 203, "config": "windows-release-arm64", "r": "4.6.2", "check": "WARNING", "artifact": "13085254754" }, { "job": 125802770814, "time": 115, "config": "windows-release-x86_64", "r": "4.6.2", "check": "WARNING", "artifact": "13085711602" } ], "_bioccheck": { "error": 2, "warning": 6, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661", "_commit": { "id": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379707 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "hexbin", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-13", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.79.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.78.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "microarray", "snpsandgeneticvariability", "snp", "geneticvariability" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 482, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 590, "source": "https://www.bioconductor.org/packages/stats/bioc/chopsticks" }, "_mentions": 1, "_searchresults": 8, "_abi": { "exports": [ { "key": "chopsticks::X.snp", "hash": "5a93d642c9efc32c" }, { "key": "chopsticks::X.snp.matrix", "hash": "5ddf3c968b211e28" }, { "key": "chopsticks::generic:ld.with", "hash": "9c6b528c0b5603fa" }, { "key": "chopsticks::genotype", "hash": "2b0f48bd04468856" }, { "key": "chopsticks::haplotype", "hash": "6b1d420ec96c11d3" }, { "key": "chopsticks::snp", "hash": "96563eaae18e5022" }, { "key": "chopsticks::snp.dprime", "hash": "113e4d9b7eafb8f1" }, { "key": "chopsticks::snp.matrix", "hash": "2ee4cc763481bb74" } ], "imports": [] }, "_rbuild": "4.6.2", "_assets": [ "extra/chopsticks.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "cbind2", "coerce", "convert.snpMatrix", "convert.snpMatrix.dir", "epsout.ld.snp", "glm.test.control", "ibs.stats", "ibsCount", "ibsDist", "initialize", "ld.snp", "ld.with", "niceprint", "pair.result.ld.snp", "plot.snp.dprime", "print.snp.dprime", "qq.chisq", "rbind2", "read.HapMap.data", "read.pedfile.info", "read.snps.chiamo", "read.snps.long", "read.snps.long.old", "read.snps.pedfile", "read.wtccc.signals", "row.summary", "show", "single.snp.tests", "snp.cbind", "snp.cor", "snp.lhs.tests", "snp.post", "snp.pre", "snp.rbind", "snp.rhs.tests", "summary", "write.snp.matrix", "xxt" ], "_datasets": [ { "name": "Asnps", "title": "Test data for the snpMatrix package", "object": "testdata", "file": "testdata.RData", "class": [ "data.frame" ], "fields": [ "rownames", "chromosome" ], "rows": 9445, "table": true, "tojson": true }, { "name": "Autosomes", "title": "Test data for the snpMatrix package", "object": "testdata", "file": "testdata.RData", "class": [ "snp.matrix" ], "fields": [], "rows": 400, "table": false, "tojson": false }, { "name": "snp.support", "title": "Data for exercise in use of the snpMatrix package", "object": "for.exercise", "file": "for.exercise.RData", "class": [ "data.frame" ], "fields": [ "chromosome", "position", "A1", "A2" ], "rows": 28501, "table": true, "tojson": true }, { "name": "snps.10", "title": "Data for exercise in use of the snpMatrix package", "object": "for.exercise", "file": "for.exercise.RData", "class": [ "snp.matrix" ], "fields": [], "rows": 1000, "table": false, "tojson": false }, { "name": "subject.data", "title": "Test data for the snpMatrix package", "object": "testdata", "file": "testdata.RData", "class": [ "data.frame" ], "fields": [ "rownames", "cc", "sex", "region" ], "rows": 400, "table": true, "tojson": true }, { "name": "subject.support", "title": "Data for exercise in use of the snpMatrix package", "object": "for.exercise", "file": "for.exercise.RData", "class": [ "data.frame" ], "fields": [ "cc", "stratum" ], "rows": 1000, "table": true, "tojson": true }, { "name": "Xchromosome", "title": "Test data for the snpMatrix package", "object": "testdata", "file": "testdata.RData", "class": [ "X.snp.matrix" ], "fields": [ "174193", "174196", "174197", "174208", "174217", "174219", "174228", "176365", "176369", "176370", "176371", "176372", "176373", "176374", "176378", "177789", "177790", "177791", "177794", "177795", "177796", "177797", "177798", "177799", "179089", "179093", "179095", "179096", "179100", "179104", "179105", "179106", "179107", "179109", "179110", "179112", "179113", "179114", "180270", "180273", "180274", "180277", "180282", "180284", "180285", "180287", "180288", "180289", "180290", "180293", "181306", "181307", "181309", "181313", "181315", "181317", "181318", "181319", "181320", "182235", "182237", "182239", "182241", "182245", "182248", "182250", "182251", "182252", "183002", "183003", "183006", "183009", "183010", "183712", "183716", "183717", "183719", "183720", "183721", "183723", "184289", "184290", "184294", "184296", "184297", "184298", "184299", "184300", "184301", "184797", "184798", "184799", "184800", "184802", "184803", "184804", "185231", "185232", "185233", "185235", "185236", "185513", "185703", "185704", "185705", "185848", "186031", "286373", "286985", "286987", "286989", "287470", "287471", "287473", "287474", "287544", "287545", "287973", "287975", "287977", "287978", "287980", "288050", "288051", "288509", "288510", "288511", "288512", "288513", "288514", "288515", "288516", "288517", "288580", "288582", "288962", "288963", "288964", "288965", "289312", "289314", "289661", "289662", "289663", "289709", "289965", "289969", "289970", "289971", "290414", "290415", "290416", "290417", "290656", "290917" ], "rows": 400, "table": false, "tojson": false }, { "name": "Xsnps", "title": "Test data for the snpMatrix package", "object": "testdata", "file": "testdata.RData", "class": [ "data.frame" ], "fields": [ "rownames" ], "rows": 155, "table": true, "tojson": true } ], "_help": [ { "page": "snpMatrix-package", "title": "The snp.matrix and X.snp.matrix classes", "topics": [ "snpMatrix-package", "snpMatrix" ] }, { "page": "epsout.ld.snp", "title": "Function to write an eps file directly to visualize LD", "topics": [ "epsout.ld.snp" ] }, { "page": "for.exercise", "title": "Data for exercise in use of the snpMatrix package", "topics": [ "for.exercise", "snp.support", "snps.10", "subject.support" ] }, { "page": "glm.test.control", "title": "Set up control object for GLM tests", "topics": [ "glm.test.control" ] }, { "page": "ibs.stats", "title": "function to calculate the identity-by-state stats of a group of samples", "topics": [ "ibs.stats" ] }, { "page": "ibsCount", "title": "Count alleles identical by state", "topics": [ "ibsCount" ] }, { "page": "ibsDist", "title": "Distance matrix based on identity by state (IBS)", "topics": [ "ibsDist" ] }, { "page": "ld.snp", "title": "Function to calculate pairwise D', $r^2$", "topics": [ "ld.snp" ] }, { "page": "ld.with", "title": "function to calculate the LD measures of specific SNPs against other SNPs", "topics": [ "ld.with", "ld.with,snp.matrix,character-method" ] }, { "page": "pair.result.ld.snp", "title": "Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPs", "topics": [ "pair.result.ld.snp" ] }, { "page": "plot.snp.dprime", "title": "Function to draw the pairwise D' in a eps file", "topics": [ "plot.snp.dprime" ] }, { "page": "qq.chisq", "title": "Quantile-quantile plot for chi-squared tests", "topics": [ "qq.chisq" ] }, { "page": "read.HapMap.data", "title": "function to import HapMap genotype data as snp.matrix", "topics": [ "read.HapMap.data" ] }, { "page": "read.pedfile.info", "title": "function to read the accompanying info file of a LINKAGE ped file", "topics": [ "read.pedfile.info" ] }, { "page": "read.pedfile.map", "title": "function to read the accompanying map file of a LINKAGE ped file", "topics": [ "read.pedfile.map" ] }, { "page": "read.snps.chiamo", "title": "Read genotype data from the output of Chiamo", "topics": [ "read.snps.chiamo" ] }, { "page": "read.snps.long", "title": "Read SNP data in long format", "topics": [ "read.snps.long" ] }, { "page": "read.snps.long.old", "title": "Read SNP input data in \"long\" format (old version)", "topics": [ "read.snps.long.old" ] }, { "page": "read.snps.pedfile", "title": "Read genotype data from a LINKAGE \"pedfile\"", "topics": [ "read.snps.pedfile" ] }, { "page": "read.wtccc.signals", "title": "read normalized signals in the WTCCC signal file format", "topics": [ "read.wtccc.signals" ] }, { "page": "row.summary", "title": "Summarize rows of a snp matrix", "topics": [ "row.summary" ] }, { "page": "single.snp.tests", "title": "1-df and 2-df tests for genetic associations with SNPs", "topics": [ "single.snp.tests" ] }, { "page": "snp-class", "title": "Class \"snp\"", "topics": [ "coerce,snp,character-method", "coerce,snp,genotype-method", "coerce,snp,numeric-method", "show,snp-method", "snp-class" ] }, { "page": "snp.cbind", "title": "Bind together two or more snp.matrix objects", "topics": [ "cbind", "cbind2", "rbind", "rbind2", "snp.cbind", "snp.rbind" ] }, { "page": "snp.cor", "title": "Correlations with columns of a snp.matrix", "topics": [ "snp.cor" ] }, { "page": "snp.dprime-class", "title": "Class \"snp.dprime\" for Results of LD calculation", "topics": [ "niceprint", "print.snp.dprime", "snp.dprime-class" ] }, { "page": "snp.lhs.tests", "title": "Score tests with SNP genotypes as dependent variable", "topics": [ "snp.lhs.tests" ] }, { "page": "snp.matrix-class", "title": "Class \"snp.matrix\"", "topics": [ "cbind,snp.matrix-method", "cbind2,snp.matrix,snp.matrix-method", "coerce,matrix,snp.matrix-method", "coerce,snp.matrix,character-method", "coerce,snp.matrix,numeric-method", "initialize,snp.matrix-method", "is.na,snp.matrix-method", "rbind,snp.matrix-method", "rbind2,snp.matrix,snp.matrix-method", "show,snp.matrix-method", "snp.matrix-class", "summary,snp.matrix-method", "[,snp.matrix,ANY,ANY,ANY-method", "[,snp.matrix-method", "[,X.snp.matrix,ANY,ANY,ANY-method" ] }, { "page": "snp.pre", "title": "Pre- or post-multiply a snp.matrix object by a general matrix", "topics": [ "snp.post", "snp.pre" ] }, { "page": "snp.rhs.tests", "title": "Score tests with SNP genotypes as independent variable", "topics": [ "snp.rhs.tests" ] }, { "page": "snpMatrix-internal", "title": "snpMatrix-internal", "topics": [ "convert.snpMatrix", "convert.snpMatrix.dir", "genotype-class", "haplotype-class" ] }, { "page": "testdata", "title": "Test data for the snpMatrix package", "topics": [ "Asnps", "Autosomes", "subject.data", "testdata", "Xchromosome", "Xsnps" ] }, { "page": "write.snp.matrix", "title": "Write a snp.matrix object as a text file", "topics": [ "write.snp.matrix" ] }, { "page": "wtccc.sample.list", "title": "read the sample list from the header of the WTCCC signal file format", "topics": [ "wtccc.sample.list" ] }, { "page": "X.snp-class", "title": "Class \"X.snp\"", "topics": [ "coerce,X.snp,character-method", "coerce,X.snp,genotype-method", "coerce,X.snp,numeric-method", "show,X.snp-method", "X.snp-class" ] }, { "page": "X.snp.matrix-class", "title": "Class \"X.snp.matrix\"", "topics": [ "coerce,snp.matrix,X.snp.matrix-method", "coerce,X.snp.matrix,character-method", "initialize,X.snp.matrix-method", "show,X.snp.matrix-method", "summary,X.snp.matrix-method", "X.snp.matrix-class", "[,X.snp.matrix-method", "[<-,X.snp.matrix,ANY,ANY,X.snp.matrix-method" ] }, { "page": "xxt", "title": "X.X-transpose for a normalised snp.matrix", "topics": [ "xxt" ] } ], "_rundeps": [ "lattice", "Matrix", "survival" ], "_vignettes": [ { "source": "chopsticks-vignette.Rnw", "filename": "chopsticks-vignette.pdf", "title": "snpMatrix", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:17:09", "modified": "2013-11-01 20:17:09", "commits": 1 } ], "_score": 3.4771212547196626, "_indexed": true, "_nocasepkg": "chopsticks", "_universes": [ "bioc", "hintak" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.79.0", "date": "2026-11-01T13:33:43.000Z", "distro": "resolute", "arch": "aarch64", "commit": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "fileid": "https://r2.ropensci.org/7a72ee55407609fadc751db694604b875c4a10925f6d8e5d0442d98fcfef7356", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661" }, { "r": "4.7.0", "os": "linux", "version": "1.79.0", "date": "2026-11-01T14:04:59.000Z", "distro": "resolute", "arch": "x86_64", "commit": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "fileid": "https://r2.ropensci.org/8fb9eed4960118971ac8dd19f6c74cbe23e1be6771b520d1040554f98fc40e55", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661" }, { "r": "4.6.2", "os": "linux", "version": "1.79.0", "date": "2026-11-01T13:33:28.000Z", "distro": "resolute", "arch": "aarch64", "commit": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "fileid": "https://r2.ropensci.org/0e0d8a056bd95ce9628556d2ae91f86fad4e8a6c608c3c1c746145643eaaf5e2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661" }, { "r": "4.6.2", "os": "linux", "version": "1.79.0", "date": "2026-11-01T14:04:57.000Z", "distro": "resolute", "arch": "x86_64", "commit": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "fileid": "https://r2.ropensci.org/a1aafbbb460311d4d66dad17e541b4ef95eb5fde5e3066a67ed108abe6b6c5d2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661" }, { "r": "4.5.3", "os": "mac", "version": "1.79.0", "date": "2026-11-01T15:43:19.000Z", "arch": "x86_64", "commit": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "fileid": "https://r2.ropensci.org/58dbb99e0beba20f000939445014f28a1aed837968438d94c59b8c5f4620afd3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661" }, { "r": "4.6.2", "os": "mac", "version": "1.79.0", "date": "2026-11-01T15:42:54.000Z", "arch": "aarch64", "commit": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "fileid": "https://r2.ropensci.org/090d69cc4cf5232e48c3a159d5f0824efbc3ff32948edaf9689b0832ac230ea4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661" }, { "r": "4.6.2", "os": "mac", "version": "1.79.0", "date": "2026-11-01T15:44:48.000Z", "arch": "x86_64", "commit": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "fileid": "https://r2.ropensci.org/dee6bb25f953ca7cd47eca6f27cd79b80717a28dd9a735b62220bbb1ac3df395", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661" }, { "r": "4.6.0", "os": "wasm", "version": "1.79.0", "date": "2026-11-01T14:03:39.000Z", "arch": "emscripten", "commit": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "fileid": "https://r2.ropensci.org/69325781e4628752adb5a074f080beb01a21f9d34329cb8caf8e21c85a27de3f", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661" }, { "r": "4.7.0", "os": "win", "version": "1.79.0", "date": "2026-11-01T13:35:26.000Z", "arch": "aarch64", "commit": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "fileid": "https://r2.ropensci.org/f7b3b8db9ab9b549fe335a04e13a2f08068f650cfabc5b00c1f63315192d0211", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661" }, { "r": "4.7.0", "os": "win", "version": "1.79.0", "date": "2026-11-01T13:40:33.000Z", "arch": "x86_64", "commit": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "fileid": "https://r2.ropensci.org/87a5dcc83865ba108955732e1bc368e209d43dc265efec5169247b18479c659f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661" }, { "r": "4.5.3", "os": "win", "version": "1.79.0", "date": "2026-11-01T13:40:34.000Z", "arch": "x86_64", "commit": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "fileid": "https://r2.ropensci.org/34fa38681ca984a5965a4d313517205affda3e351f31a7258a9f1ed74ba7771f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661" }, { "r": "4.6.2", "os": "win", "version": "1.79.0", "date": "2026-11-01T13:34:15.000Z", "arch": "aarch64", "commit": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "fileid": "https://r2.ropensci.org/ebd9097746017e168e21e64d467a575301762c6331fe7fe8ec9bc0d450bc7a69", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661" }, { "r": "4.6.2", "os": "win", "version": "1.79.0", "date": "2026-11-01T13:40:38.000Z", "arch": "x86_64", "commit": "e86f3e6c40fe5040631e03fef0300979cc172bd3", "fileid": "https://r2.ropensci.org/e3a251deccf2ee108d4a36dcea00c08c69b12299ee0ab1d5d95f29939415912c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309530661" } ] }