{ "_id": "6ae73a911e2c7b3a4f52fdf2", "Package": "CGHbase", "Type": "Package", "Title": "CGHbase: Base functions and classes for arrayCGH data analysis.", "Version": "1.73.0", "Date": "2018-06-27", "Author": "Sjoerd Vosse, Mark van de Wiel", "Maintainer": "Mark van de Wiel ", "Description": "Contains functions and classes that are needed by arrayCGH\npackages.", "License": "GPL", "Collate": "allGeneric.R classes.R private.R tools.R methods-cghRaw.R\nmethods-cghSeg.R methods-cghCall.R methods-cghRegions.R", "biocViews": "Infrastructure, Microarray, CopyNumberVariation", "URL": "https://github.com/tgac-vumc/CGHbase", "BugReports": "https://github.com/tgac-vumc/CGHbase/issues", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:32:55 UTC", "RemoteUrl": "https://github.com/bioc/CGHbase", "RemoteRef": "HEAD", "RemoteSha": "961838b43950e59b15f2b096834130c58c7ecafc", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-01 12:53:51 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "CGHbase_1.73.0.tar.gz", "_fileid": "https://r2.ropensci.org/1733944331ef3bff673355744b51632a32d562b24fdee93197280350593928bf", "_filesize": 1018359, "_sha256": "1733944331ef3bff673355744b51632a32d562b24fdee93197280350593928bf", "_expires": "2027-02-09T13:11:43.000Z", "_created": "2026-11-01T12:53:51.000Z", "_published": "2026-11-01T13:11:45.223Z", "_upstream": "https://github.com/bioc/CGHbase", "_status": "success", "_maintainer": { "name": "Mark van de Wiel", "email": "mark.vdwiel@vumc.nl", "login": "markvdwiel", "description": "", "uuid": 18324895 }, "_jobs": [ { "job": 124854281551, "time": 168, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13084835656" }, { "job": 124854281577, "time": 187, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13085015147" }, { "job": 124854281545, "time": 183, "config": "linux-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13085025103" }, { "job": 124854281627, "time": 110, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "13085061002" }, { "job": 124854281629, "time": 117, "config": "macos-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13085290103" }, { "job": 124853732648, "time": 145, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13084128255" }, { "job": 124854281566, "time": 95, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13083949378" }, { "job": 124854281582, "time": 79, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13083829849" }, { "job": 124854281606, "time": 83, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13084472717" }, { "job": 124854281598, "time": 64, "config": "windows-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13084326950" } ], "_bioccheck": { "error": 3, "warning": 5, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41308463578", "_commit": { "id": "961838b43950e59b15f2b096834130c58c7ecafc", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379575 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "Biobase", "version": ">= 2.5.5", "role": "Depends" }, { "package": "marray", "role": "Depends" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 10, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.73.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.72.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "infrastructure", "microarray", "copynumbervariation" ], "_stars": 0, "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 482, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 977, "source": "https://www.bioconductor.org/packages/stats/bioc/CGHbase" }, "_mentions": 2, "_devurl": "https://github.com/tgac-vumc/cghbase", "_searchresults": 5, "_abi": { "exports": [ { "key": "CGHbase::cghCall", "hash": "10d2e32b04e2549b" }, { "key": "CGHbase::cghRaw", "hash": "7e18b275b2ee7199" }, { "key": "CGHbase::cghRegions", "hash": "e7524010bb1c1188" }, { "key": "CGHbase::cghSeg", "hash": "f791d299c7e5f0bb" }, { "key": "CGHbase::generic:avedist", "hash": "48dd5ed699291b1b" }, { "key": "CGHbase::generic:bpend", "hash": "b93eeba742f41bf8" }, { "key": "CGHbase::generic:bpstart", "hash": "9391842798cd57cc" }, { "key": "CGHbase::generic:calls", "hash": "d17d88dcd5c826b8" }, { "key": "CGHbase::generic:calls<-", "hash": "c8da86d474424014" }, { "key": "CGHbase::generic:chromosomes", "hash": "8b73a3f7d2449576" }, { "key": "CGHbase::generic:copynumber", "hash": "3d070f7362047750" }, { "key": "CGHbase::generic:copynumber<-", "hash": "3967a6ed13922b7e" }, { "key": "CGHbase::generic:frequencyPlot", "hash": "f4b222f0c5143b78" }, { "key": "CGHbase::generic:nclone", "hash": "8296815799a9a3ce" }, { "key": "CGHbase::generic:plot.cghCall", "hash": "854893df9105941e" }, { "key": "CGHbase::generic:plot.cghRaw", "hash": "4ca5e8fd711598ea" }, { "key": "CGHbase::generic:plot.cghRegions", "hash": "abe41ebabbfcd34c" }, { "key": "CGHbase::generic:plot.cghSeg", "hash": "996c9c1630acd961" }, { "key": "CGHbase::generic:probamp", "hash": "e75f927dcf2f4015" }, { "key": "CGHbase::generic:probamp<-", "hash": "e15b1a2dc3d64b9e" }, { "key": "CGHbase::generic:probdloss", "hash": "28cc01e6d124f564" }, { "key": "CGHbase::generic:probdloss<-", "hash": "a9e462e3d13db059" }, { "key": "CGHbase::generic:probgain", "hash": "dbbbce75c0a2117c" }, { "key": "CGHbase::generic:probgain<-", "hash": "f5056efb2651eb7a" }, { "key": "CGHbase::generic:probloss", "hash": "e624e1adba81d24f" }, { "key": "CGHbase::generic:probloss<-", "hash": "8d265dbc926bb14c" }, { "key": "CGHbase::generic:probnorm", "hash": "5e94c78de00e8226" }, { "key": "CGHbase::generic:probnorm<-", "hash": "81e0310b8aeb6c26" }, { "key": "CGHbase::generic:regions", "hash": "c6690ae9f3efc22c" }, { "key": "CGHbase::generic:regions<-", "hash": "b9b7297d5222fc12" }, { "key": "CGHbase::generic:segmented", "hash": "3f3843f36fea3042" }, { "key": "CGHbase::generic:segmented<-", "hash": "19b5b128690fd1bf" } ], "imports": [ { "key": "Biobase::Versioned", "hash": "85bb92eb18e2854f" }, { "key": "Biobase::VersionedBiobase", "hash": "13a8ac2c79a1328e" }, { "key": "Biobase::eSet", "hash": "f5a727537605d4e0" } ] }, "_rbuild": "4.6.2", "_assets": [ "extra/CGHbase.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf" ], "_homeurl": "https://github.com/tgac-vumc/cghbase", "_realowner": "bioc", "_cranurl": false, "_exports": [ "avedist", "bpend", "bpstart", "calls", "calls<-", "chromosomes", "copynumber", "copynumber<-", "frequencyPlot", "frequencyPlotCalls", "initialize", "make_cghRaw", "nclone", "plot", "plot.cghCall", "plot.cghRaw", "plot.cghRegions", "plot.cghSeg", "probamp", "probamp<-", "probdloss", "probdloss<-", "probgain", "probgain<-", "probloss", "probloss<-", "probnorm", "probnorm<-", "regions", "regions<-", "segmented", "segmented<-", "summaryPlot" ], "_datasets": [ { "name": "Wilting", "title": "Cervical cancer arrayCGH data", "object": "Wilting", "file": "Wilting.txt.gz", "class": [ "data.frame" ], "fields": [ "BAC.clone", "CHROMOSOME", "START_POS", "END_POS", "AdCA10", "SCC27", "SCC32", "SCC36", "SCC39" ], "rows": 4127, "table": true, "tojson": true }, { "name": "WiltingCalled", "title": "Cervical cancer arrayCGH data called with CGHcall", "object": "WiltingCalled", "file": "WiltingCalled.rda", "class": [ "cghCall" ], "fields": [], "table": false, "tojson": false }, { "name": "WiltingNorm", "title": "Normalized log2 ratios from cervical cancer arrayCGH data.", "object": "WiltingNorm", "file": "WiltingNorm.rda", "class": [ "cghRaw" ], "fields": [], "table": false, "tojson": false }, { "name": "WiltingRaw", "title": "Raw log2 ratios from cervical cancer arrayCGH data.", "object": "WiltingRaw", "file": "WiltingRaw.rda", "class": [ "cghRaw" ], "fields": [], "table": false, "tojson": false }, { "name": "WiltingRegions", "title": "Regions of cervical cancer arrayCGH data as defined by CGHregions", "object": "WiltingRegions", "file": "WiltingRegions.rda", "class": [ "cghRegions" ], "fields": [], "table": false, "tojson": false }, { "name": "WiltingSeg", "title": "Segmented log2 ratios from cervical cancer arrayCGH data.", "object": "WiltingSeg", "file": "WiltingSeg.rda", "class": [ "cghSeg" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "CGHbase-package", "title": "CGHbase: Base functions and classes for arrayCGH data analysis.", "topics": [ "CGHbase-package", "CGHbase" ] }, { "page": "avedist", "title": "Retrieve regions information from cghRegions object.", "topics": [ "avedist", "nclone" ] }, { "page": "class.cghCall", "title": "Class to contain and describe called array comparative genomic hybridization data.", "topics": [ "bpend,cghCall-method", "bpstart,cghCall-method", "calls,cghCall-method", "calls<-,cghCall,matrix-method", "cghCall", "cghCall-class", "chromosomes,cghCall-method", "class:cghCall", "copynumber,cghCall-method", "copynumber<-,cghCall,matrix-method", "frequencyPlotCalls,cghCall,missing-method", "initialize,cghCall-method", "plot,cghCall,missing-method", "plot.summary,cghCall,missing-method", "probamp,cghCall-method", "probamp<-,cghCall,matrix-method", "probdloss,cghCall-method", "probdloss<-,cghCall,matrix-method", "probgain,cghCall-method", "probgain<-,cghCall,matrix-method", "probloss,cghCall-method", "probloss<-,cghCall,matrix-method", "probnorm,cghCall-method", "probnorm<-,cghCall,matrix-method", "segmented,cghCall-method", "segmented<-,cghCall,matrix-method" ] }, { "page": "class.cghRaw", "title": "Class to contain and describe raw or normalized array comparative genomic hybridization data.", "topics": [ "bpend,cghRaw-method", "bpstart,cghRaw-method", "cghRaw", "cghRaw-class", "chromosomes,cghRaw-method", "class:cghRaw", "copynumber,cghRaw-method", "copynumber<-,cghRaw,matrix-method", "initialize,cghRaw-method", "plot,cghRaw,missing-method" ] }, { "page": "class.cghRegions", "title": "Class to contain and describe array comparative genomic hybridization regions data.", "topics": [ "avedist,cghRegions-method", "bpend,cghRegions-method", "bpstart,cghRegions-method", "cghRegions", "cghRegions-class", "chromosomes,cghRegions-method", "class:cghRegions", "frequencyPlot,cghRegions,missing-method", "initialize,cghRegions-method", "nclone,cghRegions-method", "plot.cghRegions,cghRegions,missing-method", "regions,cghRegions-method", "regions<-,cghRegions,matrix-method" ] }, { "page": "class.cghSeg", "title": "Class to contain and describe segmented array comparative genomic hybridization data.", "topics": [ "bpend,cghSeg-method", "bpstart,cghSeg-method", "cghSeg", "cghSeg-class", "chromosomes,cghSeg-method", "class:cghSeg", "copynumber,cghSeg-method", "copynumber<-,cghSeg,matrix-method", "initialize,cghSeg-method", "plot,cghSeg,missing-method", "segmented,cghSeg-method", "segmented<-,cghSeg,matrix-method" ] }, { "page": "chromosomes", "title": "Retrieve feature position data from cgh objects.", "topics": [ "bpend", "bpstart", "chromosomes" ] }, { "page": "copynumber", "title": "Retrieve copynumber data from cgh objects.", "topics": [ "calls", "calls<-", "copynumber", "copynumber<-", "segmented", "segmented<-" ] }, { "page": "frequencyPlot", "title": "Visualization of aCGH regions.", "topics": [ "frequencyPlot" ] }, { "page": "frequencyPlotCalls", "title": "Visualization of aCGH profiles.", "topics": [ "frequencyPlotCalls" ] }, { "page": "make_cghRaw", "title": "Convert a dataframe or textfile to an object of class cghRaw.", "topics": [ "make_cghRaw" ] }, { "page": "plot", "title": "Plot aCGH data.", "topics": [ "plot.cghCall", "plot.cghRaw", "plot.cghRegions", "plot.cghSeg" ] }, { "page": "probloss", "title": "Retrieve call probabilities from a cghCall object.", "topics": [ "probamp", "probamp<-", "probdloss", "probdloss<-", "probgain", "probgain<-", "probloss", "probloss<-", "probnorm", "probnorm<-" ] }, { "page": "regions", "title": "Retrieve regions data from cghRegions object.", "topics": [ "regions", "regions<-" ] }, { "page": "summaryPlot", "title": "Visualization of aCGH profiles.", "topics": [ "summaryPlot" ] }, { "page": "Wilting", "title": "Cervical cancer arrayCGH data", "topics": [ "Wilting" ] }, { "page": "WiltingCalled", "title": "Cervical cancer arrayCGH data called with CGHcall", "topics": [ "WiltingCalled" ] }, { "page": "WiltingNorm", "title": "Normalized log2 ratios from cervical cancer arrayCGH data.", "topics": [ "WiltingNorm" ] }, { "page": "WiltingRaw", "title": "Raw log2 ratios from cervical cancer arrayCGH data.", "topics": [ "WiltingRaw" ] }, { "page": "WiltingRegions", "title": "Regions of cervical cancer arrayCGH data as defined by CGHregions", "topics": [ "WiltingRegions" ] }, { "page": "WiltingSeg", "title": "Segmented log2 ratios from cervical cancer arrayCGH data.", "topics": [ "WiltingSeg" ] } ], "_rundeps": [ "Biobase", "BiocGenerics", "generics", "limma", "marray", "statmod" ], "_score": 4.079181246047625, "_indexed": true, "_nocasepkg": "cghbase", "_universes": [ "bioc", "markvdwiel", "tgac-vumc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.73.0", "date": "2026-11-01T12:58:13.000Z", "distro": "resolute", "commit": "961838b43950e59b15f2b096834130c58c7ecafc", "fileid": "https://r2.ropensci.org/06debb89b48809e5c1c0feabc0b2395378d61d2e0ab40d5c605f3fcf87277a8b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308463578" }, { "r": "4.6.2", "os": "linux", "version": "1.73.0", "date": "2026-11-01T12:58:09.000Z", "distro": "resolute", "commit": "961838b43950e59b15f2b096834130c58c7ecafc", "fileid": "https://r2.ropensci.org/e219a91e490e69927cc97be67960185395035d95e8c13787ef9602a9e8459e66", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308463578" }, { "r": "4.5.3", "os": "mac", "version": "1.73.0", "date": "2026-11-01T13:04:43.000Z", "commit": "961838b43950e59b15f2b096834130c58c7ecafc", "fileid": "https://r2.ropensci.org/4dbc96fb60b4dca17be5052fd6f87e7548b570780b6d86c039276904543ee432", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308463578" }, { "r": "4.6.2", "os": "mac", "version": "1.73.0", "date": "2026-11-01T13:05:13.000Z", "commit": "961838b43950e59b15f2b096834130c58c7ecafc", "fileid": "https://r2.ropensci.org/05872c3acc0018a7797834d1ffc131b374e702965f36e81652da2b61526b5c8e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308463578" }, { "r": "4.6.0", "os": "wasm", "version": "1.73.0", "date": "2026-11-01T12:57:07.000Z", "commit": "961838b43950e59b15f2b096834130c58c7ecafc", "fileid": "https://r2.ropensci.org/b54aba297c77eeaed666e28430a2dd3d1d4e42671284ea8e3540974ae28091cb", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308463578" }, { "r": "4.7.0", "os": "win", "version": "1.73.0", "date": "2026-11-01T12:56:20.000Z", "commit": "961838b43950e59b15f2b096834130c58c7ecafc", "fileid": "https://r2.ropensci.org/f6a8278a9d693f21fe7cc24681523d99eacb35a9750159d9b3ef66df46fcc3a1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308463578" }, { "r": "4.5.3", "os": "win", "version": "1.73.0", "date": "2026-11-01T12:56:26.000Z", "commit": "961838b43950e59b15f2b096834130c58c7ecafc", "fileid": "https://r2.ropensci.org/7183b2d506a2f4c95724544ee8c8f7faeb3cf81f82d98d714e3fb14eb4d93d58", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308463578" }, { "r": "4.6.2", "os": "win", "version": "1.73.0", "date": "2026-11-01T12:56:15.000Z", "commit": "961838b43950e59b15f2b096834130c58c7ecafc", "fileid": "https://r2.ropensci.org/237dcc855639ad328fa6317b8952269ec487ab6bd3ac355ddf57469f0cfddca2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308463578" } ] }