Man pages for CoreGx
Classes and Functions to Serve as the Basis for Other 'Gx' Packages
| amcc | Calculate an Adaptive Matthews Correlation Coefficient |
| as | LongTable to data.table conversion |
| as.data.frame.LongTable | Coerce a LongTable to a data.frame |
| as.data.table.LongTable | Coerce a LongTable into a 'data.table' |
| as.long.table | Coerce from data.table to LongTable |
| assayCols | Generic to access the assay columns of a rectangular object. |
| buildLongTable | Build a LongTable object |
| callingWaterfall | Drug sensitivity calling using waterfall plots |
| cash-LongTable-method | Select an assay from a LongTable object |
| cellInfo | cellInfo Getter |
| cellInfo-set | cellInfo<- Generic |
| cellNames | cellNames Generic |
| cellNames-set | cellNames<- Generic |
| checkCsetStructure | A function to verify the structure of a CoreSet |
| clevelandSmall_cSet | Cleaveland_mut RadioSet subsetted and cast as CoreSet |
| colIDs | Generic to access the row identifiers for an object. |
| colMeta | Generic to access the column identifiers for a rectangular... |
| connectivityScore | Function computing connectivity scores between two signatures |
| CoreSet | CoreSet constructor |
| CoreSet-class | A Superclass to Contain Data for Genetic Profiling and... |
| cosinePerm | Cosine Permutations |
| Create | LongTable build method from list |
| curation | curation Slot Getter |
| curation-set | curation<- Slot Setter |
| datasetType | datasetType Generic |
| datasetType-set | datasetType<- Replacement Generic |
| dateCreated | dateCreated Generic |
| dateCreated-set | dateCreated<- Generic |
| dot- | Convenience function for converting R code to a call |
| 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-intersectList | Intersect A List of More Than Two Vectors |
| 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... |
| drugSensitivitySig | Compute the correlation between a molecular feature and... |
| featureInfo | featureInfo Generic |
| featureInfo-set | featureInfo<- Generic |
| fNames | fNames Generic |
| fNames-set | fNames<- Generic |
| getIntern | Retrieve the symbol for the object@.intern slot |
| gwc | GWC Score |
| idCols | Generic to access the unique id columns in an S4 object used... |
| idCols-LongTable-method | Retrieve the unique identifier columns used for primary keys... |
| is.items | Get the types of all items in a list |
| list_or_LongTable-class | A class union to allow multiple types in a CoreSet slot |
| LongTable | LongTable constructor method |
| LongTable-class | LongTable class definition |
| mcc | Compute a Mathews Correlation Coefficient |
| mDataNames | mDataNames Generic |
| mDataNames-set | mDataNames<- Generic |
| merckLongTable | Merck Drug Combination Data LongTable |
| 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 |
| molecularProfiles | molecularProfiles Generic |
| molecularProfiles-set | molecularProfiles<- Generic |
| molecularProfilesSlot | molecularProfilesSlot Generic |
| molecularProfilesSlot-set | molecularProfilesSlot<- |
| name | name Generic |
| name-set | name<- Generic |
| pertNumber | pertNumber Generic |
| pertNumber-set | pertNumber<- Generic |
| phenoInfo | phenoInfo Generic |
| phenoInfo-set | phenoInfo<- Generic |
| RadioSet | annotation<- Slot Setter |
| reindex | Generic method for resetting indexing in an S4 object |
| reindex-LongTable-method | Redo indexing for a LongTable object to remove any gaps in... |
| 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 |
| sensitivitySlot | sensitivitySlot Generic |
| sensitivitySlot-set | sensitivitySlot<- Replacement Generic |
| sensitivitySlotToLongTable | sensitivitySlotToLongTable Generic |
| sensNumber | sensNumber Generic |
| sensNumber-set | sensNumber<- Generic |
| show-CoreSet-method | Show a CoreSet |
| show-LongTable-method | Ensure that all rowID and colID keys are valid |
| 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... |
| summarizeMolecularProfiles | Summarize molecular profile data such that there is a single... |
| summarizeSensitivityProfiles | Summarize across replicates for a sensitivity dose-response... |
| updateCellId | Update the cell ids in a cSet object |
