Man pages for bhklab/CoreGx
Classes and Functions to Serve as the Basis for Other 'Gx' Packages
| aggregate2 | Functional API for data.table aggregation which allows... |
| aggregate-data.table-method | Functional S4 API for aggregation over a 'data.table' object. |
| aggregate-LongTable-method | Functional API for aggregation over a 'LongTable' or... |
| amcc | Calculate an Adaptive Matthews Correlation Coefficient |
| as | Coerce a 'LongTable' to a 'TreatmentResponseExperiment' |
| as.long.table | Coerce from data.table to LongTable |
| assayCols | Generic to access the assay columns of a rectangular object. |
| assayIndex | Retrieve and assayIndex |
| assayKeys | Retrieve a set of assayKeys |
| assay-LongTableDataMapper-ANY-method | Extract the data for an assay from a 'LongTableDataMapper' |
| assays-LongTableDataMapper-method | Extract the data for all assays from a 'LongTableDataMapper' |
| assays-TREDataMapper-method | Extract the data for all assays from a 'TREDataMapper' |
| assay-TREDataMapper-ANY-method | Extract the data for an assay from a 'TREDataMapper' |
| assignment-immutable | Intercept assignment operations for "immutable" S3 objects. |
| buildComboProfiles | Build an assay table with an 'S4' object. |
| buildComboProfiles-LongTable-method | Build an assay table with selected assay profiles for drug... |
| buildLongTable | Build a LongTable object |
| buildLongTable-character-method | LongTable build method from character |
| buildLongTable-data.frame-method | LongTable build method |
| buildLongTable-list-method | LongTable build method from list |
| callingWaterfall | Drug sensitivity calling using waterfall plots |
| cash-LongTable-method | Select an assay from a LongTable object |
| cash-set-LongTable-method | Update an assay from a LongTable object |
| checkColumnCardinality | Search a data.frame for 1:'cardinality' relationships between... |
| checkCsetStructure | A function to verify the structure of a CoreSet |
| c.immutable | Intercept concatenation for "immutable" class objects to... |
| clevelandSmall_cSet | Cleaveland_mut RadioSet subsetted and cast as CoreSet |
| colData-LongTableDataMapper-method | Convenience method to subset the 'colData' out of the... |
| colData-TREDataMapper-method | Convenience method to subset the 'colData' out of the... |
| colIDs | Generic to access the row identifiers for an object. |
| collect_fn_params | Collects all function arguments other than the first into a... |
| colMeta | Generic to access the column identifiers for a rectangular... |
| connectivityScore | Function computing connectivity scores between two signatures |
| CoreGx-deprecated | List of 'deprecated' or 'defunct' methods in the 'CoreGx' R... |
| CoreSet | CoreSet constructor |
| CoreSet2 | Make a CoreSet with the updated class structure |
| CoreSet-accessors | Accessing and modifying information in a 'CoreSet' |
| CoreSet-class | CoreSet - A generic data container for molecular profiles and... |
| CoreSet-utils | Utility methods for a 'CoreSet' object. |
| cosinePerm | Cosine Permutations |
| DataMapper-accessors | Accessing and modifying data in a 'DataMapper' object. |
| DataMapper-class | An S4 Class For Mapping from Raw Experimental Data to a... |
| dot- | Convenience function for converting R code to a call |
| dot-assayToBumpyMatrix | Convert a LongTable assay into a BumpyMatrix object |
| dot-convertCSetMolecularProfilesToSE | CSet molecularProfiles from ESets to SEs |
| dot-distancePointLine | Calculate shortest distance between point and line |
| dot-distancePointSegment | Calculate shortest distance between point and line segment |
| dot-fitCurve2 | Curve fitting via 'stats::optim' L-BFGS-B with fall-back... |
| dot-intersectList | Intersect A List of More Than Two Vectors |
| dot-longTableToSummarizedExperiment | Convert LongTable to gDR Style SummarizedExperiment |
| dot-symSetDiffList | Utility to find the symmetric set difference of a list of two... |
| dot-unionList | Utility to find the union between a list of more than two... |
| drop_fn_params | Drop parameters from a function and replace them with... |
| drugSensitivitySig | Compute the correlation between a molecular feature and... |
| endoaggregate | Perform aggregation over an S4 object, but return an object... |
| endoaggregate-LongTable-method | Functional API for endomorphic aggregation over a 'LongTable'... |
| exampleDataMapper | Example LongTableDataMapper |
| getIntern | Retrieve the specified item from object internal metadata. |
| getIntern-set | Set the internal structural metadata for an S4 class |
| getIntern-set-LongTable-immutable_list-method | Set the .intern slot of a LongTable |
| guessMapping | Generic for Guessing the Mapping Between Some Raw Data and an... |
| guessMapping-LongTableDataMapper-method | Guess which columns in raw experiment data map to which... |
| gwc | GWC Score |
| idCols | Generic to access the unique id columns in an S4 object used... |
| immutable | Constructor for "immutable" S3-class property |
| is.items | Get the types of all items in a list |
| is_optim_compatible | Check whether a function signature is amenable to... |
| lapply-MultiAssayExperiment-method | lapply lapply method for 'MultiAssayExperiment' |
| list_OR_LongTable-class | A class union to allow multiple types in a CoreSet slot |
| LongTable | LongTable constructor method |
| LongTable-accessors | Accessing and modifying information in a 'LongTable' |
| LongTable-class | LongTable class definition |
| LongTableDataMapper | Constructor for the 'LongTableDataMapper' class, which maps... |
| LongTableDataMapper-accessors | Accessing and modifying data in a 'LongTableDataMapper'... |
| LongTableDataMapper-class | A Class for Mapping Between Raw Data and an 'LongTable'... |
| make_optim_function | Takes a non-primitive R function and refactors it to be... |
| mcc | Compute a Mathews Correlation Coefficient |
| merckLongTable | Merck Drug Combination Data LongTable |
| mergeAssays | Merge assays with an 'S4' object. |
| mergeAssays-LongTable-method | Endomorphically merge assays within a 'LongTable' or... |
| metaConstruct | Generic for preprocessing complex data before being used in... |
| metadata-LongTable-method | Getter method for the metadata slot of a 'LongTable' object |
| metadata-set-LongTable-method | Setter method for the metadata slot of a 'LongTable' object |
| mutable | Remove the "immutable" S3-class from an R object, allowing it... |
| nci_TRE_small | NCI-ALMANAC Drug Combination Data TreatmentResponseExperiment... |
| optimizeCoreGx | A helper method to find the best multithreading configuration... |
| printSlot | Helper function to print slot information |
| reindex | Generic method for resetting indexing in an S4 object |
| reindex-LongTable-method | Redo indexing for a LongTable object to remove any gaps in... |
| rowData-LongTableDataMapper-method | Convenience method to subset the 'rowData' out of the... |
| rowData-TREDataMapper-method | Convenience method to subset the 'rowData' out of the... |
| rowIDs | Generic to access the row identifiers from |
| rowMeta | Generic to access the row identifiers from |
| sensitivityInfo | Generic function to get the annotations for a treatment... |
| sensitivityInfo-set | sensitivityInfo<- Generic Method |
| sensitivityMeasures | sensitivityMeasures Generic |
| sensitivityMeasures-set | sensitivityMeasures<- Generic |
| sensitivityProfiles | sensitivityProfiles Generic |
| sensitivityProfiles-set | sensitivityProfiles<- Generic |
| sensitivityRaw | sensitivityRaw Generic Method |
| sensitivityRaw-set | sensitivityRaw<- Generic |
| sensitivitySlotToLongTable | sensitivitySlotToLongTable Generic |
| setOps-immutable | Subset an immutable object, returning another immutable... |
| show-CoreSet-method | Show a CoreSet |
| show-LongTable-method | Show method for the LongTable class |
| showSigAnnot | Get the annotations for a 'Signature' class object, as... |
| sub-LongTable-ANY-ANY-ANY-method | [ LongTable Method |
| subset-LongTable-method | Subset method for a LongTable object. |
| subsetTo | Subset a CoreSet object based on various parameters, such as... |
| sub-subset-LongTable-ANY-ANY-method | [[<- Method for LongTable Class |
| summarizeMolecularProfiles | Summarize molecular profile data such that there is a single... |
| summarizeSensitivityProfiles | Summarize across replicates for a sensitivity dose-response... |
| TreatmentResponseExperiment | TreatmentResponseExperiment constructor method |
| TreatmentResponseExperiment-class | TreatmentResponseExperiment class definition |
| TREDataMapper | Constructor for the 'TREDataMapper' class, which maps from... |
| TREDataMapper-accessors | Accessing and modifying data in a 'TREDataMapper' object. |
| TREDataMapper-class | A Class for Mapping Between Raw Data and an... |
| updateObject-CoreSet-method | Update the 'CoreSet' class after changes in it struture or... |
| updateObject-LongTable-method | Update the 'LongTable' class after changes in it struture or... |
| updateSampleId | Update the sample ids in a cSet object |
| updateTreatmentId | Update the treatment ids in a cSet object |
