{ "_id": "6a494963a788432aeabf4886", "Package": "CNAnorm", "Version": "1.59.0", "Date": "2012-08-06", "Title": "A normalization method for Copy Number Aberration in cancer\nsamples", "Author": "Stefano Berri , Henry M. Wood\n, Arief Gusnanto ", "Maintainer": "Stefano Berri ", "Description": "Performs ratio, GC content correction and normalization of\ndata obtained using low coverage (one read every 100-10,000 bp)\nhigh troughput sequencing. It performs a \"discrete\"\nnormalization looking for the ploidy of the genome. It will\nalso provide tumour content if at least two ploidy states can\nbe found.", "License": "GPL-2", "Collate": "AllGenerics.R AllClasses.R dataFrame2object.R\nworkflowWrapper.R initialize-methods.R summary-methods.R\nsmoothseg.R bandsegment.R mixtureModel.R normalize.R\nlength-methods.R CNAnorm-accessors.R CNAnorm-methods.R\nData-methods.R makeDefaultGraphParamteres.R", "URL": "http://www.r-project.org,", "LazyLoad": "yes", "Packaged": { "Date": "2026-07-03 14:16:27 UTC", "User": "root" }, "biocViews": "CopyNumberVariation, Sequencing, Coverage, Normalization,\nWholeGenome, DNASeq, GenomicVariation", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:35:53 UTC", "RemoteUrl": "https://github.com/bioc/CNAnorm", "RemoteRef": "HEAD", "RemoteSha": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "NeedsCompilation": "yes", "_user": "bioc", "_type": "src", "_file": "CNAnorm_1.59.0.tar.gz", "_fileid": "https://r2.ropensci.org/256129d078f158ec0ec0cfc7d158dcd9b2687c60ddaa74191ac00cca9dc875bd", "_filesize": 1645032, "_sha256": "256129d078f158ec0ec0cfc7d158dcd9b2687c60ddaa74191ac00cca9dc875bd", "_expires": "2026-10-12T17:56:49.000Z", "_created": "2026-07-03T14:16:27.000Z", "_published": "2026-07-04T17:56:51.631Z", "_bioccheck": { "error": 2, "warning": 4, "note": 11 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28666014160", "_status": "success", "_upstream": "https://github.com/bioc/CNAnorm", "_commit": { "id": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379753 }, "_maintainer": { "name": "Stefano Berri", "email": "sberri@illumina.com" }, "_distro": "resolute", "_jobs": [ { "job": 85154149385, "time": 137, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8068797623" }, { "job": 85154149288, "time": 146, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "8068802401" }, { "job": 85154149414, "time": 143, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8068799991" }, { "job": 85154149445, "time": 133, "config": "linux-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8068797619" }, { "job": 85154149336, "time": 194, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8068817312" }, { "job": 85154149282, "time": 143, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8068799913" }, { "job": 85154149240, "time": 165, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "8068806977" }, { "job": 85154149268, "time": 88, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8068780720" }, { "job": 85154149225, "time": 261, "config": "macos-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8068840645" }, { "job": 85154149121, "time": 164, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8068749071" }, { "job": 85154149210, "time": 98, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8068783833" }, { "job": 85154149306, "time": 90, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8068781685" }, { "job": 85154149246, "time": 91, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8068781594" }, { "job": 85154149254, "time": 86, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8068780303" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10.1", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "DNAcopy", "role": "Imports" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.59.0", "bioc": "3.24" }, { "branch": "release", "version": "1.58.0", "bioc": "3.23" } ], "_topics": [ "copynumbervariation", "sequencing", "coverage", "normalization", "wholegenome", "dnaseq", "genomicvariation" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 21, "_searchresults": 9, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CNAnorm.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "addDNACopy", "addSmooth", "arms", "chrs", "chrs<-", "CNAnormWorkflow", "dataFrame2object", "discreteNorm", "exportTable", "gcNorm", "peakPloidy", "plotGenome", "plotPeaks", "pos", "pos<-", "ratio", "ratio.n", "ratio.s", "ratio.s.n", "segMean", "segMean.n", "sugg.peaks", "sugg.ploidy", "valid.peaks", "valid.ploidy", "validation" ], "_datasets": [ { "name": "CN", "title": "A CNAnorm object with information about most abundant ploidy states, obtained from data LS041.", "object": "CN", "file": "CN.RData", "class": [ "CNAnorm" ], "fields": [], "table": false, "tojson": false }, { "name": "gPar", "title": "An object with the default graphical parameters", "object": "gPar", "file": "gPar.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "hg19_hs_ideogr", "title": "An object with the ideogram information for homo sapiens - hg19", "object": "hg19_hs_ideogr", "file": "hg19_hs_ideogr.RData", "class": [ "data.frame" ], "fields": [ "chrom", "chromStart", "chromEnd", "name", "gieStain" ], "rows": 862, "table": true, "tojson": true }, { "name": "LS041", "title": "Mapped reads in tumor and matched blood for patient LS041", "object": "LS041", "file": "LS041.RData", "class": [ "data.frame" ], "fields": [ "Chr", "Pos", "Test", "Norm", "GC" ], "rows": 7262, "table": true, "tojson": true } ], "_help": [ { "page": "addDNACopy-methods", "title": "Methods for Function addDNACopy in Package `CNAnorm'", "topics": [ "addDNACopy", "addDNACopy,CNAnorm-method", "addDNACopy-methods" ] }, { "page": "addSmooth-methods", "title": "Methods for Function addSmooth in Package `CNAnorm'", "topics": [ "addSmooth", "addSmooth,CNAnorm-method", "addSmooth-methods" ] }, { "page": "chrsAndpos-methods", "title": "Accessors methods for Function ratio in Package `CNAnorm'", "topics": [ "arms", "arms,CNAnorm-method", "arms-methods", "chrs", "chrs-methods", "chrs<-", "chrs<--methods", "pos", "pos,CNAnorm-method", "pos-methods", "pos<-", "pos<--methods" ] }, { "page": "CN", "title": "A CNAnorm object with information about most abundant ploidy states, obtained from data LS041.", "topics": [ "CN" ] }, { "page": "CNAnorm-class", "title": "Class \"CNAnorm\"", "topics": [ "chrs,CNAnorm-method", "chrs<-,CNAnorm-method", "CNAnorm", "CNAnorm-class", "length,CNAnorm-method", "pos<-,CNAnorm-method", "ratio,CNAnorm-method", "ratio.n,CNAnorm-method", "ratio.s,CNAnorm-method", "ratio.s.n,CNAnorm-method", "segMean,CNAnorm-method", "segMean.n,CNAnorm-method", "sugg.peaks,CNAnorm-method", "sugg.ploidy,CNAnorm-method", "valid.peaks,CNAnorm-method", "valid.ploidy,CNAnorm-method", "[,CNAnorm-method" ] }, { "page": "workflowWrapper", "title": "Wrapper to '\"CNAnorm\"' workflow", "topics": [ "CNAnormWorkflow" ] }, { "page": "dataFrame2object", "title": "Convert a data frame into an object of Class '\"CNAnorm\"'", "topics": [ "dataFrame2object" ] }, { "page": "DerivData-class", "title": "Class \"DerivData\"", "topics": [ "DerivData-class", "length,DerivData-method" ] }, { "page": "discreteNorm-methods", "title": "Methods for Function addSmooth in Package `CNAnorm'", "topics": [ "discreteNorm", "discreteNorm,CNAnorm-method", "discreteNorm-methods" ] }, { "page": "exportTable-method", "title": "Methods for Function exportTable in Package `CNAnorm'", "topics": [ "exportTable", "exportTable,CNAnorm-method", "exportTable-methods" ] }, { "page": "gcNorm-methods", "title": "Methods for Function gcNorm in Package `CNAnorm'", "topics": [ "gcNorm", "gcNorm,CNAnorm-method", "gcNorm-methods" ] }, { "page": "gPar", "title": "An object with the default graphical parameters", "topics": [ "gPar" ] }, { "page": "data-hg19_hs_ideogr", "title": "An object with the ideogram information for homo sapiens - hg19", "topics": [ "hg19_hs_ideogr" ] }, { "page": "InData-class", "title": "Class \"InData\" ~~~", "topics": [ "InData-class", "length,InData-method" ] }, { "page": "LS041", "title": "Mapped reads in tumor and matched blood for patient LS041", "topics": [ "LS041" ] }, { "page": "Params-class", "title": "Class \"Params\"", "topics": [ "Params-class" ] }, { "page": "peakPloidy", "title": "Methods for Function peakPloidy in Package `CNAnorm'", "topics": [ "peakPloidy", "peakPloidy,CNAnorm-method", "peakPloidy-methods" ] }, { "page": "plotGenome-methods", "title": "Methods for Function plotGenome in Package `CNAnorm'", "topics": [ "plotGenome", "plotGenome,CNAnorm-method", "plotGenome-methods" ] }, { "page": "plotPeaks-methods", "title": "Methods for Function plotPeaks in Package `CNAnorm'", "topics": [ "plotPeaks", "plotPeaks,CNAnorm-method", "plotPeaks-methods" ] }, { "page": "ratio-methods", "title": "Methods for Function ratio in Package `CNAnorm'", "topics": [ "ratio", "ratio-methods", "ratio.n", "ratio.n-methods", "ratio.s", "ratio.s-methods", "ratio.s.n", "ratio.s.n-methods", "segMean", "segMean-methods", "segMean.n", "segMean.n-methods" ] }, { "page": "suggValid-methods", "title": "Methods for Function to retrieve suggested/validated ploidy and peaks in Package `CNAnorm'", "topics": [ "sugg.peaks", "sugg.peaks-methods", "sugg.ploidy", "sugg.ploidy-methods", "valid.peaks", "valid.peaks-methods", "valid.ploidy", "valid.ploidy-methods" ] }, { "page": "validation-methods", "title": "Methods for Function addSmooth in Package `CNAnorm'", "topics": [ "validation", "validation,CNAnorm-method", "validation-methods" ] } ], "_rundeps": [ "DNAcopy" ], "_vignettes": [ { "source": "CNAnorm.Snw", "filename": "CNAnorm.pdf", "title": "An introduction to CNAnorm", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:21:19", "modified": "2014-03-05 16:55:42", "commits": 3 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "cnanorm", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.59.0", "date": "2026-07-03T14:18:55.000Z", "distro": "resolute", "arch": "aarch64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "https://r2.ropensci.org/748de2ab0da183e3eb2a838f1b555622021f60918c9e1ce4f2accab340f65829", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28666014160" }, { "r": "4.7.0", "os": "linux", "version": "1.59.0", "date": "2026-07-03T14:18:46.000Z", "distro": "resolute", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "https://r2.ropensci.org/e6d600080f650ab45106683af06084995836b094ca6eee095881a01a11ca1109", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28666014160" }, { "r": "4.6.1", "os": "linux", "version": "1.59.0", "date": "2026-07-03T14:18:43.000Z", "distro": "resolute", "arch": "aarch64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "https://r2.ropensci.org/82bd9178d2d924c62303765137d9cfeec46865354eedaf3a9bd92959c651e285", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28666014160" }, { "r": "4.6.1", "os": "linux", "version": "1.59.0", "date": "2026-07-03T14:19:33.000Z", "distro": "resolute", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "https://r2.ropensci.org/0ddb88cdfa7943c475dc8b49f6a012c797bd1b11efe265f96d1a34e2e103d99a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28666014160" }, { "r": "4.5.3", "os": "mac", "version": "1.59.0", "date": "2026-07-03T14:18:37.000Z", "arch": "aarch64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "https://r2.ropensci.org/e516750d673408de5c01f8f8eb1335204779bdd048ebb5afd9796ef3951556e7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28666014160" }, { "r": "4.5.3", "os": "mac", "version": "1.59.0", "date": "2026-07-03T14:18:50.000Z", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "https://r2.ropensci.org/46a69cdd1373b9f16b02ea47c78bbb3d2c003d12f30d096e05e07d0c91a26625", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28666014160" }, { "r": "4.6.1", "os": "mac", "version": "1.59.0", "date": "2026-07-03T14:17:54.000Z", "arch": "aarch64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "https://r2.ropensci.org/d1e2c9bf375e8a4c74eae7a61456a0a8e7861ede65e8fa4aca2b16075432cde6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28666014160" }, { "r": "4.6.1", "os": "mac", "version": "1.59.0", "date": "2026-07-03T14:20:02.000Z", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "https://r2.ropensci.org/5e05f9287b1c8b189b30e444e0c60581c0311f0d115634c19d962fadfd072fcb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28666014160" }, { "r": "4.6.0", "os": "wasm", "version": "1.59.0", "date": "2026-07-03T14:18:24.000Z", "arch": "emscripten", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "https://r2.ropensci.org/ec36f0a400825445ab860a4d69c24742934389d4c22e2e22663fa619437705c1", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28666014160" }, { "r": "4.7.0", "os": "win", "version": "1.59.0", "date": "2026-07-03T14:17:35.000Z", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "https://r2.ropensci.org/059f808c7e36f516d2885a183515350cacea6b1f322e7850fb87d779943a2c35", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28666014160" }, { "r": "4.5.3", "os": "win", "version": "1.59.0", "date": "2026-07-03T14:17:36.000Z", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "https://r2.ropensci.org/9ca796f0bc33615bb76fbfc03dfbeb390fd695f4d7a34c72a44154a9e7f60060", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28666014160" }, { "r": "4.6.1", "os": "win", "version": "1.59.0", "date": "2026-07-03T14:17:31.000Z", "arch": "x86_64", "commit": "48ad80c66d0b1f60f02d1f0590d19a5b00bc69e4", "fileid": "https://r2.ropensci.org/062fbac699ea5508a46b126a2991b15e882f9a9f749566e37ba42637f4db3b04", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28666014160" } ] }