{ "_id": "6a1e9f431d7bb097a0a70069", "Package": "coloc", "Type": "Package", "Title": "Colocalisation Tests of Two Genetic Traits", "Version": "6.0.1", "Date": "2025-11-19", "Authors@R": "c(person(\"Chris\", \"Wallace\", role=c(\"aut\",\"cre\"), email = \"cew54@cam.ac.uk\"),\nperson(\"Claudia\",\"Giambartolomei\", role=\"aut\", email=\"claudia.giambartolomei.10@ucl.ac.uk\"),\nperson(\"Vincent\",\"Plagnol\", role=\"ctb\", email=\"v.plagnol@ucl.ac.uk\"),\nperson(\"Tom\",\"Willis\", role=\"aut\", email=\"tom.willis@live.com\"),\nperson(\"Jeffrey\",\"Pullin\", role=\"aut\", email=\"jp2045@cam.ac.uk\"))", "Maintainer": "Chris Wallace ", "Description": "Performs the colocalisation tests described in\nGiambartolomei et al (2013) ,\nWallace (2020) , Wallace\n(2021) , Pullin and Wallace\n(2025) .", "License": "GPL", "LazyLoad": "yes", "VignetteBuilder": "knitr", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "URL": "https://github.com/chr1swallace/coloc,\nhttps://chr1swallace.github.io/coloc/", "BugReports": "https://github.com/chr1swallace/coloc/issues", "Collate": "'coloc-package.R' 'boundaries.R' 'check.R' 'claudia.R'\n'plot.R' 'private.R' 'sensitivity.R' 'split.R' 'susie.R'\n'data.R' 'zzz.R'", "LazyData": "true", "Repository": "https://chr1swallace.r-universe.dev", "Date/Publication": "2025-12-04 12:41:58 UTC", "RemoteUrl": "https://github.com/chr1swallace/coloc", "RemoteRef": "HEAD", "RemoteSha": "50fe5291fea7f8ab49823bd86747385d6e56870f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 09:08:24 UTC", "User": "root" }, "Author": "Chris Wallace [aut, cre],\nClaudia Giambartolomei [aut],\nVincent Plagnol [ctb],\nTom Willis [aut],\nJeffrey Pullin [aut]", "MD5sum": "016667460525bc3fc4bdfd7fb226d5f8", "_user": "chr1swallace", "_type": "src", "_file": "coloc_6.0.1.tar.gz", "_fileid": "44762c4c21f1d3ba4746a887f2eeec630231a51cf8946f45f3707d6488c50879", "_filesize": 6884899, "_sha256": "44762c4c21f1d3ba4746a887f2eeec630231a51cf8946f45f3707d6488c50879", "_created": "2026-06-02T09:08:24.000Z", "_published": "2026-06-02T09:15:47.588Z", "_distro": "noble", "_jobs": [ { "job": 79037240247, "time": 293, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7353653001" }, { "job": 79037240241, "time": 378, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7353683637" }, { "job": 79037240280, "time": 212, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7353617540" }, { "job": 79037240178, "time": 206, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7353615448" }, { "job": 79036203851, "time": 363, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7353548769" }, { "job": 79037240259, "time": 263, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7353643009" }, { "job": 79037240196, "time": 267, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7353643897" }, { "job": 79037240245, "time": 193, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7353619256" }, { "job": 79037240254, "time": 229, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7353631173" } ], "_buildurl": "https://github.com/r-universe/chr1swallace/actions/runs/26809702344", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/chr1swallace/coloc", "_commit": { "id": "50fe5291fea7f8ab49823bd86747385d6e56870f", "author": "Chris Wallace ", "committer": "Chris Wallace ", "message": "new pgkdown\n", "time": 1764852118 }, "_maintainer": { "name": "Chris Wallace", "email": "cew54@cam.ac.uk", "login": "chr1swallace", "description": "Statisitician using genomics to understand immune-mediated diseases. Github hosts mainly R packages to do statistical analysis of genetic data.", "uuid": 2189544 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "susieR", "version": ">= 0.12.06", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "mvtnorm", "role": "Suggests" }, { "package": "magrittr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "EnsDb.Hsapiens.v86", "role": "Suggests" }, { "package": "EnsDb.Hsapiens.v75", "role": "Suggests" }, { "package": "locuszoomr", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" } ], "_owner": "chr1swallace", "_selfowned": true, "_usedby": 3, "_updates": [ { "week": "2025-31", "n": 1 }, { "week": "2025-47", "n": 3 }, { "week": "2025-49", "n": 1 } ], "_tags": [], "_stars": 199, "_contributors": [ { "user": "chr1swallace", "count": 262, "uuid": 2189544 }, { "user": "twillis209", "count": 8, "uuid": 30097448 }, { "user": "jeffreypullin", "count": 6, "uuid": 34267114 }, { "user": "grealesm", "count": 3, "uuid": 7490028 }, { "user": "jdblischak", "count": 3, "uuid": 1608317 }, { "user": "vplagnol", "count": 3, "uuid": 977542 }, { "user": "hui-guo", "count": 2, "uuid": 6011272 }, { "user": "olivroy", "count": 1, "uuid": 52606734 } ], "_userbio": { "uuid": 2189544, "type": "user", "name": "Chris Wallace", "description": "Statisitician using genomics to understand immune-mediated diseases. Github hosts mainly R packages to do statistical analysis of genetic data." }, "_downloads": { "count": 3264, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/coloc" }, "_mentions": 49, "_devurl": "https://github.com/chr1swallace/coloc", "_pkgdown": "https://chr1swallace.github.io/coloc/", "_searchresults": 1320, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/coloc.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/chr1swallace/coloc", "_realowner": "chr1swallace", "_cranurl": true, "_releases": [ { "version": "1.05", "date": "2012-01-04" }, { "version": "1.07", "date": "2012-02-22" }, { "version": "1.08", "date": "2012-04-12" }, { "version": "1.10", "date": "2012-11-30" }, { "version": "1.11", "date": "2013-01-25" }, { "version": "2.0", "date": "2013-05-23" }, { "version": "2.1", "date": "2013-06-03" }, { "version": "2.2", "date": "2013-06-19" }, { "version": "2.3", "date": "2013-09-25" }, { "version": "2.3-1", "date": "2013-09-29" }, { "version": "3.1", "date": "2018-02-24" }, { "version": "3.2-1", "date": "2019-05-17" }, { "version": "5.1.0", "date": "2021-06-14" }, { "version": "5.1.0.1", "date": "2022-07-05" }, { "version": "5.2.2", "date": "2023-05-12" }, { "version": "5.2.3", "date": "2023-10-03" } ], "_exports": [ "annotate_susie", "check_alignment", "check_dataset", "check.alignment", "check.dataset", "coloc.abf", "coloc.bf_bf", "coloc.signals", "coloc.susie", "coloc.susie_bf", "credible.sets", "findends", "finemap.abf", "finemap.bf", "finemap.signals", "plot_dataset", "plot_datasets", "plot_extended_datasets", "process.dataset", "runsusie", "sensitivity", "subset_dataset" ], "_datasets": [ { "name": "coloc_test_data", "title": "Simulated data to use in testing and vignettes in the coloc package", "object": "coloc_test_data", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "eqtlgen_density_data", "title": "eQTLGen estimated distance density", "object": "eqtlgen_density_data", "class": [ "data.frame" ], "fields": [ "rel_dist", "dens_value" ], "rows": 512, "table": true, "tojson": true } ], "_help": [ { "page": "coloc-package", "title": "Colocalisation tests of two genetic traits", "topics": [ "-package", "coloc-package" ] }, { "page": "annotate_susie", "title": "annotate susie_rss output for use with coloc_susie", "topics": [ "annotate_susie" ] }, { "page": "approx.bf.estimates", "title": "Internal function, approx.bf.estimates", "topics": [ "approx.bf.estimates" ] }, { "page": "approx.bf.p", "title": "Internal function, approx.bf.p", "topics": [ "approx.bf.p" ] }, { "page": "bin2lin", "title": "binomial to linear regression conversion", "topics": [ "bin2lin" ] }, { "page": "check_alignment", "title": "check alignment", "topics": [ "check.alignment", "check_alignment" ] }, { "page": "check_dataset", "title": "check_dataset", "topics": [ "check.dataset", "check_dataset" ] }, { "page": "coloc_test_data", "title": "Simulated data to use in testing and vignettes in the coloc package", "topics": [ "coloc_test_data" ] }, { "page": "coloc.abf", "title": "Fully Bayesian colocalisation analysis using Bayes Factors", "topics": [ "coloc.abf" ] }, { "page": "coloc.bf_bf", "title": "Coloc data through Bayes factors", "topics": [ "coloc.bf_bf" ] }, { "page": "coloc.detail", "title": "Bayesian colocalisation analysis with detailed output", "topics": [ "coloc.detail" ] }, { "page": "coloc.process", "title": "Post process a coloc.details result using masking", "topics": [ "coloc.process" ] }, { "page": "coloc.signals", "title": "Coloc with multiple signals per trait", "topics": [ "coloc.signals" ] }, { "page": "coloc.susie", "title": "run coloc using susie to detect separate signals", "topics": [ "coloc.susie" ] }, { "page": "coloc.susie_bf", "title": "run coloc using susie to detect separate signals", "topics": [ "coloc.susie_bf" ] }, { "page": "combine.abf", "title": "combine.abf", "topics": [ "combine.abf" ] }, { "page": "credible.sets", "title": "credible.sets", "topics": [ "credible.sets" ] }, { "page": "eqtlgen_density_data", "title": "eQTLGen estimated distance density", "topics": [ "eqtlgen_density_data" ] }, { "page": "est_cond", "title": "generate conditional summary stats", "topics": [ "est_cond" ] }, { "page": "estgeno1", "title": "estgeno1", "topics": [ "estgeno.1.cse", "estgeno.1.ctl" ] }, { "page": "find.best.signal", "title": "Pick out snp with most extreme Z score", "topics": [ "find.best.signal" ] }, { "page": "findends", "title": "trim a dataset to central peak(s)", "topics": [ "findends" ] }, { "page": "findpeaks", "title": "trim a dataset to only peak(s)", "topics": [ "findpeaks" ] }, { "page": "finemap.abf", "title": "Bayesian finemapping analysis", "topics": [ "finemap.abf" ] }, { "page": "finemap.bf", "title": "Finemap data through Bayes factors", "topics": [ "finemap.bf" ] }, { "page": "finemap.signals", "title": "Finemap multiple signals in a single dataset", "topics": [ "finemap.signals" ] }, { "page": "logbf_to_pp", "title": "logbf 2 pp", "topics": [ "logbf_to_pp" ] }, { "page": "logdiff", "title": "logdiff", "topics": [ "logdiff" ] }, { "page": "logsum", "title": "logsum", "topics": [ "logsum" ] }, { "page": "map_cond", "title": "find the next most significant SNP, conditioning on a list of sigsnps", "topics": [ "map_cond" ] }, { "page": "map_mask", "title": "find the next most significant SNP, masking a list of sigsnps", "topics": [ "map_mask" ] }, { "page": "plot_dataset", "title": "plot a coloc dataset", "topics": [ "plot_dataset" ] }, { "page": "plot_datasets", "title": "plot a pair of coloc datasets, highlighting the snps that are common between them", "topics": [ "plot_datasets" ] }, { "page": "plot_extended_datasets", "title": "Draw extended plot of summary statistics for two coloc datasets", "topics": [ "plot_extended_datasets" ] }, { "page": "plot-methods", "title": "plot a coloc_abf object", "topics": [ "plot.coloc_abf" ] }, { "page": "print-methods", "title": "print.coloc_abf", "topics": [ "print.coloc_abf" ] }, { "page": "process.dataset", "title": "process.dataset", "topics": [ "process.dataset" ] }, { "page": "runsusie", "title": "Run susie on a single coloc-structured dataset", "topics": [ "runsusie" ] }, { "page": "sdY.est", "title": "Estimate trait variance, internal function", "topics": [ "sdY.est" ] }, { "page": "sensitivity", "title": "Prior sensitivity for coloc", "topics": [ "sensitivity" ] }, { "page": "subset_dataset", "title": "subset_dataset", "topics": [ "subset_dataset" ] }, { "page": "Var.data", "title": "Var.data", "topics": [ "Var.data" ] }, { "page": "Var.data.cc", "title": "Var.data", "topics": [ "Var.data.cc" ] } ], "_pkglogo": "https://github.com/chr1swallace/coloc/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/chr1swallace/coloc/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "crayon", "data.table", "farver", "ggplot2", "glue", "gridExtra", "gtable", "irlba", "isoband", "labeling", "lattice", "lifecycle", "Matrix", "matrixStats", "mixsqp", "plyr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape", "rlang", "S7", "scales", "susieR", "vctrs", "viridis", "viridisLite", "withr" ], "_vignettes": [ { "source": "a01_intro.Rmd", "filename": "a01_intro.html", "title": "Coloc: a package for colocalisation analyses", "author": "Chris Wallace", "engine": "knitr::rmarkdown", "headings": [ "A brief outline of colocalisation analysis", "A single causal variant assumption", "Sensitivity analysis", "Deprecated: relaxing the single causal variant assumption through conditioning", "An improved approach to relaxing the single causal variant assumption: SuSiE", "Footnotes" ], "created": "2019-07-08 09:20:38", "modified": "2023-05-12 10:53:25", "commits": 7 }, { "source": "a02_data.Rmd", "filename": "a02_data.html", "title": "Coloc: data structures", "author": "Chris Wallace", "engine": "knitr::rmarkdown", "headings": [ "Data structures", "First: select the SNPs to study.", "A minimum coloc dataset", "Analysing two datasets", "What if I don't have sdY?", "What if I don't have beta and/or varbeta?", "Additional LD information for coloc.susie", "NB studies from different populations", "NB allele order matters!" ], "created": "2021-03-23 12:50:40", "modified": "2025-11-19 09:41:37", "commits": 9 }, { "source": "a04_sensitivity.Rmd", "filename": "a04_sensitivity.html", "title": "Coloc: sensitivity to prior values", "author": "Chris Wallace", "engine": "knitr::rmarkdown", "headings": [ "Sensitivity analysis" ], "created": "2019-07-08 09:20:38", "modified": "2021-06-08 17:47:43", "commits": 5 }, { "source": "a03_enumeration.Rmd", "filename": "a03_enumeration.html", "title": "Coloc: under a single causal variant assumption", "author": "Chris Wallace", "engine": "knitr::rmarkdown", "headings": [ "Fine mapping under a single causal variant assumption", "(Approximate) Bayes Factor colocalisation analyses", "Introduction", "The basic coloc.abf function" ], "created": "2019-07-08 09:20:38", "modified": "2021-06-08 17:47:43", "commits": 6 }, { "source": "a06_SuSiE.Rmd", "filename": "a06_SuSiE.html", "title": "Coloc: using SuSiE to relax the single causal variant assumption", "author": "Chris Wallace", "engine": "knitr::rmarkdown", "headings": [ "Multiple causal variants, using SuSiE to separate the signals", "Important notes on running SuSiE" ], "created": "2021-03-22 11:39:04", "modified": "2022-05-05 19:48:49", "commits": 8 }, { "source": "a07_variant-specific-priors.Rmd", "filename": "a07_variant-specific-priors.html", "title": "Coloc: using variant-specific priros in coloc", "author": "Jeffrey Pullin", "engine": "knitr::rmarkdown", "headings": [ "Variant-specific priors in coloc", "Using general variant-specific information", "An example of variant-specific information" ], "created": "2025-03-27 17:07:03", "modified": "2025-03-27 17:21:09", "commits": 2 }, { "source": "a05_conditioning.Rmd", "filename": "a05_conditioning.html", "title": "DEPRECATED Coloc: relaxing the single causal variant assumption", "author": "Chris Wallace", "engine": "knitr::rmarkdown", "headings": [ "Multiple causal variants" ], "created": "2019-07-08 09:20:38", "modified": "2022-03-21 10:58:56", "commits": 4 } ], "_score": 12.753707006220901, "_indexed": true, "_nocasepkg": "coloc", "_universes": [ "chr1swallace" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "6.0.1", "date": "2026-06-02T09:13:02.000Z", "distro": "noble", "commit": "50fe5291fea7f8ab49823bd86747385d6e56870f", "fileid": "4a90e597d71d4437beb71dc74a81105bbfa895e1182be49205ba647f09a7f7b9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/chr1swallace/actions/runs/26809702344" }, { "r": "4.6.0", "os": "linux", "version": "6.0.1", "date": "2026-06-02T09:14:27.000Z", "distro": "noble", "commit": "50fe5291fea7f8ab49823bd86747385d6e56870f", "fileid": "85707d5678b6fe43d3ad6f0f1d37227aafeca561d148440cccb2895526264a43", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/chr1swallace/actions/runs/26809702344" }, { "r": "4.5.3", "os": "mac", "version": "6.0.1", "date": "2026-06-02T09:11:43.000Z", "commit": "50fe5291fea7f8ab49823bd86747385d6e56870f", "fileid": "3ea6866f8489e845594672697948ef5240ee7862988e3a2a8f211edbbcedadda", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/chr1swallace/actions/runs/26809702344" }, { "r": "4.6.0", "os": "mac", "version": "6.0.1", "date": "2026-06-02T09:11:30.000Z", "commit": "50fe5291fea7f8ab49823bd86747385d6e56870f", "fileid": "c32b5df7d1972acb64ad464cbe8d1f141e65a9edf2aa9d260a22c2aac4b72863", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/chr1swallace/actions/runs/26809702344" }, { "r": "4.6.0", "os": "wasm", "version": "6.0.1", "date": "2026-06-02T09:13:32.000Z", "commit": "50fe5291fea7f8ab49823bd86747385d6e56870f", "fileid": "cd30ccff3f6110db2779a41ef3de2c4d4cc7157e505b2ba0ace0dab98e27221b", "status": "success", "buildurl": "https://github.com/r-universe/chr1swallace/actions/runs/26809702344" }, { "r": "4.7.0", "os": "win", "version": "6.0.1", "date": "2026-06-02T09:12:30.000Z", "commit": "50fe5291fea7f8ab49823bd86747385d6e56870f", "fileid": "feaaa9431a509eb1b93a96d2df7e842809f39b960f4faae293e57c18c39c6c7d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/chr1swallace/actions/runs/26809702344" }, { "r": "4.5.3", "os": "win", "version": "6.0.1", "date": "2026-06-02T09:11:14.000Z", "commit": "50fe5291fea7f8ab49823bd86747385d6e56870f", "fileid": "6249ab8770f9607f8bc2307f0b19ef1f639226c578192104489058a029973cf8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/chr1swallace/actions/runs/26809702344" }, { "r": "4.6.0", "os": "win", "version": "6.0.1", "date": "2026-06-02T09:11:46.000Z", "commit": "50fe5291fea7f8ab49823bd86747385d6e56870f", "fileid": "8cadb299247fe2e4799e5f890f31695d49b9ac264aca364474d2d551d969db2b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/chr1swallace/actions/runs/26809702344" } ] }