{ "_id": "6a33a08c3efcd9bda43a868e", "Package": "MultiDataSet", "Type": "Package", "Title": "Implementation of MultiDataSet and ResultSet", "Version": "1.40.0", "Date": "2021-10-04", "Authors@R": "c(person(\"Carlos\", \"Ruiz-Arenas\", , \"carlos.ruiz@isglobal.org\", role = c(\"aut\", \"cre\")),\nperson(\"Carles\", \"Hernandez-Ferrer\", , \"carles.hernandez@isglobal.org\", role = \"aut\"),\nperson(\"Juan R.\", \"Gonzalez\", ,\"juanr.gonzalez@isglobal.org\", role = \"aut\"))", "Maintainer": "Xavier Escrib Montagut ", "Description": "Implementation of the BRGE's (Bioinformatic Research Group\nin Epidemiology from Center for Research in Environmental\nEpidemiology) MultiDataSet and ResultSet. MultiDataSet is\ndesigned for integrating multi omics data sets and ResultSet is\na container for omics results. This package contains base\nclasses for MEAL and rexposome packages.", "License": "file LICENSE", "LazyData": "TRUE", "biocViews": "Software, DataRepresentation", "RoxygenNote": "7.1.0", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:43:25 UTC", "RemoteUrl": "https://github.com/bioc/MultiDataSet", "RemoteRef": "RELEASE_3_23", "RemoteSha": "bde2f4121b385b8bbecea94adfe72725fb540085", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-18 07:16:08 UTC", "User": "root" }, "Author": "Carlos Ruiz-Arenas [aut, cre],\nCarles Hernandez-Ferrer [aut],\nJuan R. Gonzalez [aut]", "MD5sum": "b92a94df2662ac5d50e3d685170ba10b", "_user": "bioc-release", "_type": "src", "_file": "MultiDataSet_1.40.0.tar.gz", "_fileid": "9f600f133ba9341763c392ce1511a51236bec12f9c6d51335d1806778df28332", "_filesize": 228267, "_sha256": "9f600f133ba9341763c392ce1511a51236bec12f9c6d51335d1806778df28332", "_created": "2026-06-18T07:16:08.000Z", "_published": "2026-06-18T07:38:52.442Z", "_jobs": [ { "job": 82075289895, "time": 442, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7716725752" }, { "job": 82075289886, "time": 577, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7716766079" }, { "job": 82075289897, "time": 558, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7716760730" }, { "job": 82075289901, "time": 337, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7717001945" }, { "job": 82075289891, "time": 333, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7716998961" }, { "job": 82074217985, "time": 422, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7716589951" }, { "job": 82075289879, "time": 402, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7716713434" }, { "job": 82075289936, "time": 471, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7716735125" }, { "job": 82075289906, "time": 385, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7716707615" }, { "job": 82075289920, "time": 392, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7716710172" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742908146", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/MultiDataSet", "_commit": { "id": "bde2f4121b385b8bbecea94adfe72725fb540085", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380205 }, "_maintainer": { "name": "Xavier Escribà Montagut", "email": "xavier.escriba@isglobal.org" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "qqman", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "brgedata", "role": "Suggests" }, { "package": "minfi", "role": "Suggests" }, { "package": "minfiData", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "omicade4", "role": "Suggests" }, { "package": "iClusterPlus", "role": "Suggests" }, { "package": "GEOquery", "role": "Suggests" }, { "package": "MultiAssayExperiment", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "RaggedExperiment", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 11, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.41.0", "bioc": "3.24" }, { "branch": "release", "version": "1.40.0", "bioc": "3.23" } ], "_topics": [ "software", "datarepresentation" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 5, "_searchresults": 29, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MultiDataSet.html", "extra/NEWS.html", "extra/NEWS.txt", "LICENSE", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "add_eset", "add_genexp", "add_methy", "add_rnaseq", "add_rse", "add_se", "add_snps", "add_table", "as.list", "chrNumToChar", "commonIds", "commonSamples", "create_resultset", "createMultiDataSet", "getAssociation", "lambdaClayton", "mae2mds", "mds2mae", "opt", "plot", "qq_plot", "rowRanges", "rowRangesElements", "volcano_plot", "w_iclusterplus", "w_mcia" ], "_datasets": [ { "name": "rset", "title": "Example 'ResultSet'", "object": "rset", "class": [ "ResultSet" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "add_eset", "title": "Method to add an 'eSet' to 'MultiDataSet'.", "topics": [ "add_eset" ] }, { "page": "add_genexp", "title": "Method to add an expression microarray dataset to 'MultiDataSet'.", "topics": [ "add_genexp" ] }, { "page": "add_methy", "title": "Method to add a slot of methylation to 'MultiDataSet'.", "topics": [ "add_methy" ] }, { "page": "add_rnaseq-methods", "title": "Method to add an expression RNA seq dataset to 'MultiDataSet'.", "topics": [ "add_rnaseq" ] }, { "page": "add_rse", "title": "Method to add a 'RangedSummarizedExperiment' to 'MultiDataSet'.", "topics": [ "add_rse" ] }, { "page": "add_se", "title": "Method to add a 'SummarizedExperiment' to 'MultiDataSet'.", "topics": [ "add_se" ] }, { "page": "add_snps", "title": "Method to add a slot of SNPs to 'MultiDataSet'.", "topics": [ "add_snps" ] }, { "page": "add_table", "title": "Method to add a 'matrix' to 'MultiDataSet'.", "topics": [ "add_table" ] }, { "page": "chrNumToChar", "title": "Convert chr numbers to chr strings", "topics": [ "chrNumToChar" ] }, { "page": "commonIds", "title": "Get the name of the ids common to all datasets", "topics": [ "commonIds" ] }, { "page": "commonSamples", "title": "Method to select samples that are present in all datasets.", "topics": [ "commonSamples" ] }, { "page": "getAssociation-methods", "title": "Method to extrat feature result from a ResultSet", "topics": [ "getAssociation" ] }, { "page": "lambdaClayton", "title": "Lambda Calculation for a vector of P-Values", "topics": [ "lambdaClayton" ] }, { "page": "mae2mds", "title": "Convert a 'MultiAssayExperiment' to a 'MultiDataSet'", "topics": [ "mae2mds" ] }, { "page": "mds2mae", "title": "Convert a 'MultiDataSet' to a 'MultiAssayExperiment'", "topics": [ "mds2mae" ] }, { "page": "MultiDataSet", "title": "MultiDataSet: Implementation of the BRGE's basic classes", "topics": [ "MultiDataSet" ] }, { "page": "MultiDataSet-class", "title": "MultiDataSet instances", "topics": [ "add_eset,MultiDataSet,eSet-method", "add_genexp,MultiDataSet,ExpressionSet-method", "add_methy,MultiDataSet,GenomicRatioSet-method", "add_rnaseq,MultiDataSet,ExpressionSet-method", "add_rse,MultiDataSet,RangedSummarizedExperiment-method", "add_se,MultiDataSet,SummarizedExperiment-method", "add_snps,MultiDataSet,SnpSet-method", "add_table,MultiDataSet,matrix-method", "as.list", "as.list,MultiDataSet-method", "assayData", "assayData,MultiDataSet-method", "commonIds,MultiDataSet-method", "commonSamples,MultiDataSet-method", "createMultiDataSet", "dims", "dims,MultiDataSet-method", "fData", "fData,MultiDataSet-method", "featureData", "featureData,MultiDataSet-method", "length", "length,MultiDataSet-method", "MultiDataSet-class", "MultiDataSet-methods", "MultiDataSet-methods,", "names", "names,MultiDataSet-method", "ncol", "ncol,MultiDataSet-method", "nrow", "nrow,MultiDataSet-method", "pData", "pData,MultiDataSet-method", "phenoData", "phenoData,MultiDataSet-method", "rowRanges", "rowRanges,MultiDataSet-method", "rowRangesElements,MultiDataSet-method", "sampleNames,MultiDataSet-method", "subset,MultiDataSet-method", "w_iclusterplus,MultiDataSet-method", "w_mcia,MultiDataSet-method", "[", "[,MultiDataSet,ANY,ANY,ANY-method", "[[,MultiDataSet,ANY,ANY-method" ] }, { "page": "opt-methods", "title": "Method to get the options sued to create the ResultSet", "topics": [ "opt" ] }, { "page": "qq_plot", "title": "Function to draw a QQ Plot from a vector of numbers", "topics": [ "qq_plot" ] }, { "page": "ResultSet-class", "title": "Class ResultSet", "topics": [ "create_resultset", "fData,ResultSet-method", "getAssociation,ResultSet-method", "length,ResultSet-method", "names,ResultSet-method", "opt,ResultSet-method", "plot,ResultSet,ANY-method", "ResultSet", "ResultSet-class", "ResultSet-methods", "varLabels,ResultSet-method" ] }, { "page": "rowRangesElements", "title": "Get the name of the datasets that have rowRanges", "topics": [ "rowRangesElements" ] }, { "page": "rset", "title": "Example 'ResultSet'", "topics": [ "rset" ] }, { "page": "volcano_plot", "title": "Function to draw a Volcano Plot", "topics": [ "volcano_plot" ] }, { "page": "w_iclusterplus", "title": "Apply iClusterPlus clustering method to a MultiDataSet object", "topics": [ "w_iclusterplus" ] }, { "page": "w_mcia", "title": "Apply mcia integration method to a MultiDataSet object", "topics": [ "w_mcia" ] } ], "_rundeps": [ "abind", "Biobase", "BiocGenerics", "calibrate", "cli", "cpp11", "DelayedArray", "farver", "generics", "GenomicRanges", "ggplot2", "ggrepel", "glue", "gtable", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "limma", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "qqman", "R6", "RColorBrewer", "Rcpp", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SparseArray", "statmod", "SummarizedExperiment", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "MultiDataSet_Extending_Proteome.Rmd", "filename": "MultiDataSet_Extending_Proteome.html", "title": "Adding a new type of data to MultiDataSet objects", "author": "Carles Hernandez-Ferrer, Carlos Ruiz-Arenas, Alba Beltran-Gomila, Juan R. González", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Objective", "Implementation", "Defining ProteomeSet", "Loading Proteome Data", "Extending MultiDataSet", "Data example: Adding Proteome data to MultiDataSet objects" ], "created": "2017-02-27 15:49:58", "modified": "2021-10-07 13:34:50", "commits": 7 }, { "source": "MultiDataSet.Rmd", "filename": "MultiDataSet.html", "title": "Introduction to MultiDataSet", "author": "| Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain | Bioinformatics Research Group in Epidemiology | (http://www.creal.cat/brge.htm)", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Create a new MultiDataSet", "Adding sets", "General functions", "Add eSet", "Add SummarizedExperiment", "Specific functions", "Subsetting", "Samples", "Tables", "GenomicRanges", "Multiple subsetting", "Advanced subsetting" ], "created": "2017-02-21 15:40:26", "modified": "2018-02-15 14:19:38", "commits": 7 } ], "_score": 6.281941933440825, "_indexed": false, "_nocasepkg": "multidataset", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/MultiDataSet", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.40.0", "date": "2026-06-18T07:23:52.000Z", "distro": "noble", "commit": "bde2f4121b385b8bbecea94adfe72725fb540085", "fileid": "0af574fb2eb908dacb0e5fc43f084d07beaebad5bd33c42973789dee06537a03", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742908146" }, { "r": "4.6.0", "os": "linux", "version": "1.40.0", "date": "2026-06-18T07:23:43.000Z", "distro": "noble", "commit": "bde2f4121b385b8bbecea94adfe72725fb540085", "fileid": "0e7935ba46748bd545e04736e4fce0c1c65360002853fb341d1f531614f0f4a6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742908146" }, { "r": "4.5.3", "os": "mac", "version": "1.40.0", "date": "2026-06-18T07:36:29.000Z", "commit": "bde2f4121b385b8bbecea94adfe72725fb540085", "fileid": "1b61614d50bec9025c17afd8d2a6699456dd6918697c29d14a90bc7a712dfce2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742908146" }, { "r": "4.6.0", "os": "mac", "version": "1.40.0", "date": "2026-06-18T07:36:19.000Z", "commit": "bde2f4121b385b8bbecea94adfe72725fb540085", "fileid": "b933ec8afe5a0f9fec44a8501894d51e5430c028088b274e3f7c31685c85f6c9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742908146" }, { "r": "4.6.0", "os": "wasm", "version": "1.40.0", "date": "2026-06-18T07:23:16.000Z", "commit": "bde2f4121b385b8bbecea94adfe72725fb540085", "fileid": "af1b488a3ebab667e7691633fcdf930d4fbd5abe65fa3d03752d57f3ca281cfa", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742908146" }, { "r": "4.7.0", "os": "win", "version": "1.40.0", "date": "2026-06-18T07:22:09.000Z", "commit": "bde2f4121b385b8bbecea94adfe72725fb540085", "fileid": "96591e31a64e68efcfe21144c1c31b43e9d1b7f221d588a5cbd9241228f2fd32", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742908146" }, { "r": "4.5.3", "os": "win", "version": "1.40.0", "date": "2026-06-18T07:20:41.000Z", "commit": "bde2f4121b385b8bbecea94adfe72725fb540085", "fileid": "2b8bd1de59e74dcd629b1ce9382aff79ef17d9e5c426750693285bd4d1545152", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742908146" }, { "r": "4.6.0", "os": "win", "version": "1.40.0", "date": "2026-06-18T07:20:48.000Z", "commit": "bde2f4121b385b8bbecea94adfe72725fb540085", "fileid": "40eef03f6452fefa45337752242c36b0ef4198278ac37cd0288b0bff836b91b8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27742908146" } ] }