{ "_id": "6a1ad5871d7bb097a09e51fc", "Package": "CoreGx", "Type": "Package", "Title": "Classes and Functions to Serve as the Basis for Other 'Gx'\nPackages", "Version": "2.17.0", "Date": "2024-03-11", "Authors@R": "c(\nperson(given=\"Jermiah\", family=\"Joseph\", email=\"jermiah.joseph@uhn.ca\",\nrole=c(\"aut\")),\nperson(given=\"Petr\", family=\"Smirnov\", email = \"petr.smirnov@uhnresearch.ca\",\nrole = c(\"aut\")),\nperson(given=\"Ian\", family=\"Smith\", email = \"ianc.smith@mail.utoronto.ca\",\nrole = c(\"aut\")),\nperson(given=\"Christopher\", family=\"Eeles\", email = \"christopher.eeles@uhnresearch.ca\",\nrole = c(\"aut\")),\nperson(given=\"Feifei\", family=\"Li\", email=\"ff.li@mail.utoronto.ca\",\nrole=c(\"aut\")),\nperson(\"Benjamin\", \"Haibe-Kains\",\nemail = \"benjamin.haibe.kains@utoronto.ca\", role = c(\"aut\", \"cre\"))\n)", "Description": "A collection of functions and classes which serve as the\nfoundation for our lab's suite of R packages, such as\n'PharmacoGx' and 'RadioGx'. This package was created to\nabstract shared functionality from other lab package releases\nto increase ease of maintainability and reduce code repetition\nin current and future 'Gx' suite programs. Major features\ninclude a 'CoreSet' class, from which 'RadioSet' and\n'PharmacoSet' are derived, along with get and set methods for\neach respective slot. Additional functions related to fitting\nand plotting dose response curves, quantifying statistical\ncorrelation and calculating area under the curve (AUC) or\nsurvival fraction (SF) are included. For more details please\nsee the included documentation, as well as: Smirnov, P.,\nSafikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C.,\nFreeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A.,\nAerts, H., Lupien, M., Goldenberg, A. (2015)\n. Manem, V., Labie, M.,\nSmirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed,\nM., Haibe-Kains, B., Bratman, S. 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'utils-optimization.R'\n'utils-testing.R' 'utils-updateS4.R'", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:52:42 UTC", "RemoteUrl": "https://github.com/bioc/CoreGx", "RemoteRef": "HEAD", "RemoteSha": "d48c63f334288d22cf320aa6fe065adf7ac66c60", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:44:41 UTC", "User": "root" }, "Author": "Jermiah Joseph [aut],\nPetr Smirnov [aut],\nIan Smith [aut],\nChristopher Eeles [aut],\nFeifei Li [aut],\nBenjamin Haibe-Kains [aut, cre]", "Maintainer": "Benjamin Haibe-Kains ", "MD5sum": "85153b3cb199e89aba762d2acd11e8f0", "_user": "bioc", "_type": "src", "_file": "CoreGx_2.17.0.tar.gz", "_fileid": "06e90473f06c74ba6c2579abdc7f5438a9e66157c01214630e388479b2dffd29", "_filesize": 1559642, "_sha256": "06e90473f06c74ba6c2579abdc7f5438a9e66157c01214630e388479b2dffd29", "_created": "2026-05-30T08:44:41.000Z", 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Permutations", "topics": [ "cosinePerm" ] }, { "page": "DataMapper-accessors", "title": "Accessing and modifying data in a 'DataMapper' object.", "concept": [ "DataMapper-accessors" ], "topics": [ "DataMapper-accessors", "rawdata", "rawdata,DataMapper-method", "rawdata<-", "rawdata<-,DataMapper,ANY-method" ] }, { "page": "DataMapper-class", "title": "An S4 Class For Mapping from Raw Experimental Data to a Specific S4 Object", "topics": [ ".DataMapper", "DataMapper-class" ] }, { "page": "drop_fn_params", "title": "Drop parameters from a function and replace them with constants inside the function body.", "topics": [ "drop_fn_params" ] }, { "page": "endoaggregate", "title": "Perform aggregation over an S4 object, but return an object of the same class.", "topics": [ "endoaggregate" ] }, { "page": "endoaggregate-LongTable-method", "title": "Functional API for endomorphic aggregation over a 'LongTable' or inheriting class", "topics": [ "endoaggregate,LongTable-method" ] }, { "page": "exampleDataMapper", "title": "Example LongTableDataMapper", "topics": [ "exampleDataMapper" ] }, { "page": "getIntern", "title": "Retrieve the specified item from object internal metadata.", "topics": [ "getIntern" ] }, { "page": "guessMapping", "title": "Generic for Guessing the Mapping Between Some Raw Data and an S4 Object", "topics": [ "guessMapping" ] }, { "page": "guessMapping-LongTableDataMapper-method", "title": "Guess which columns in raw experiment data map to which dimensions.", "topics": [ "guessMapping,LongTableDataMapper-method" ] }, { "page": "gwc", "title": "GWC Score", "topics": [ "gwc" ] }, { "page": "idCols", "title": "Generic to access the unique id columns in an S4 object used to", "topics": [ "idCols" ] }, { "page": "immutable", "title": "Constructor for \"immutable\" S3-class property", "topics": [ "immutable", "immutable_list-class", "is.immutable", "print.immutable", "show.immutable" ] }, { "page": "is_optim_compatible", "title": "Check whether a function signature is amenable to optimization via 'stats::optim'.", "topics": [ "is_optim_compatible" ] }, { "page": "is.items", "title": "Get the types of all items in a list", "topics": [ "is.items" ] }, { "page": "lapply-MultiAssayExperiment-method", "title": "lapply lapply method for 'MultiAssayExperiment'", "topics": [ "lapply,MultiAssayExperiment-method" ] }, { "page": "list_OR_LongTable-class", "title": "A class union to allow multiple types in a CoreSet slot", "topics": [ "list_OR_LongTable-class" ] }, { "page": "LongTable", "title": "LongTable constructor method", "topics": [ "LongTable" ] }, { "page": "LongTable-accessors", "title": "Accessing and modifying information in a 'LongTable'", "topics": [ "LongTable-accessors" ] }, { "page": "LongTableDataMapper", "title": "Constructor for the 'LongTableDataMapper' class, which maps from one or more raw experimental data files to the slots of a 'LongTable' object.", "topics": [ "LongTableDataMapper" ] }, { "page": "LongTableDataMapper-accessors", "title": "Accessing and modifying data in a 'LongTableDataMapper' object.", "concept": [ "DataMapper-accessors" ], "topics": [ "assayMap,LongTableDataMapper,List-method", "assayMap,LongTableDataMapper,list-method", "assayMap,LongTableDataMapper-method", "assayMap<-,LongTableDataMapper,List-methhod", "assayMap<-,LongTableDataMapper,list-method", "assayMap<-,LongTableDataMapper,list_OR_List-method", "colDataMap,LongTableDataMapper-method", "colDataMap<-,LongTableDataMapper,list_OR_List-method", "colDataMap<-LongTableDataMapper,List-method", "LongTableDataMapper-accessors", "metadataMap,LongTableDataMapper-method", "metadataMap<-,LongTableDataMapper,list_OR_List-method", "metadataMap<-,LongTableDataMapper-method", "rawdata,LongTableDataMapper-method", "rawdata<-,LongTableDataMapper,list-method", "rowDataMap,LongTableDataMapper-method", "rowDataMap<-,LongTableDataMapper,list-method", "rowDataMap<-,LongTableDataMapper,list_OR_List-method", "rowDataMap<-LongTableDataMapper,List-method" ] }, { "page": "LongTableDataMapper-class", "title": "A Class for Mapping Between Raw Data and an 'LongTable' Object", "topics": [ ".LongTableDataMapper", "LongTableDataMapper-class", "show,LongTableDataMapper-method" ] }, { "page": "make_optim_function", "title": "Takes a non-primitive R function and refactors it to be compatible with optimization via 'stats::optim'.", "topics": [ "make_optim_function" ] }, { "page": "mcc", "title": "Compute a Mathews Correlation Coefficient", "topics": [ "mcc" ] }, { "page": "merckLongTable", "title": "Merck Drug Combination Data LongTable", "topics": [ "merckLongTable" ] }, { "page": "mergeAssays", "title": "Merge assays with an 'S4' object.", "topics": [ "mergeAssays" ] }, { "page": "mergeAssays-LongTable-method", "title": "Endomorphically merge assays within a 'LongTable' or inheriting class", "topics": [ "mergeAssays,LongTable-method" ] }, { "page": "metaConstruct", "title": "Generic for preprocessing complex data before being used in the constructor of an 'S4' container object.", "topics": [ "metaConstruct", "metaConstruct,LongTableDataMapper-method", "metaConstruct,TREDataMapper-method" ] }, { "page": "metadata-LongTable-method", "title": "Getter method for the metadata slot of a 'LongTable' object", "topics": [ "metadata,LongTable-method" ] }, { "page": "metadata-set-LongTable-method", "title": "Setter method for the metadata slot of a 'LongTable' object", "topics": [ "metadata<-,LongTable-method" ] }, { "page": "mutable", "title": "Remove the \"immutable\" S3-class from an R object, allowing it to be modified normally again.", "topics": [ "mutable" ] }, { "page": "nci_TRE_small", "title": "NCI-ALMANAC Drug Combination Data TreatmentResponseExperiment Subset", "topics": [ "nci_TRE_small" ] }, { "page": "optimizeCoreGx", "title": "A helper method to find the best multithreading configuration for your computer", "topics": [ "optimizeCoreGx" ] }, { "page": "reindex", "title": "Generic method for resetting indexing in an S4 object", "topics": [ "reindex" ] }, { "page": "reindex-LongTable-method", "title": "Redo indexing for a LongTable object to remove any gaps in integer indexes", "topics": [ "reindex,LongTable-method" ] }, { "page": "rowData-LongTableDataMapper-method", "title": "Convenience method to subset the 'rowData' out of the 'rawdata' slot using the assigned 'rowDataMap' metadata.", "topics": [ "rowData,LongTableDataMapper-method" ] }, { "page": "rowData-TREDataMapper-method", "title": "Convenience method to subset the 'rowData' out of the 'rawdata' slot using the assigned 'rowDataMap' metadata.", "topics": [ "rowData,TREDataMapper-method" ] }, { "page": "rowIDs", "title": "Generic to access the row identifiers from", "topics": [ "rowIDs" ] }, { "page": "rowMeta", "title": "Generic to access the row identifiers from", "topics": [ "rowMeta" ] }, { "page": "sensitivityInfo", "title": "Generic function to get the annotations for a treatment response experiment from an S4 class", "topics": [ "sensitivityInfo" ] }, { "page": "sensitivityInfo-set", "title": "sensitivityInfo<- Generic Method", "topics": [ "sensitivityInfo<-" ] }, { "page": "sensitivityMeasures", "title": "sensitivityMeasures Generic", "topics": [ "sensitivityMeasures" ] }, { "page": "sensitivityMeasures-set", "title": "sensitivityMeasures<- Generic", "topics": [ "sensitivityMeasures<-" ] }, { "page": "sensitivityProfiles", "title": "sensitivityProfiles Generic", "topics": [ "sensitivityProfiles" ] }, { "page": "sensitivityProfiles-set", "title": "sensitivityProfiles<- Generic", "topics": [ "sensitivityProfiles<-" ] }, { "page": "sensitivityRaw", "title": "sensitivityRaw Generic Method", "topics": [ "sensitivityRaw" ] }, { "page": "sensitivityRaw-set", "title": "sensitivityRaw<- Generic", "topics": [ "sensitivityRaw<-" ] }, { "page": "sensitivitySlotToLongTable", "title": "sensitivitySlotToLongTable Generic", "topics": [ "sensitivitySlotToLongTable" ] }, { "page": 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