Man pages for CoreGx
Classes and Functions to Serve as the Basis for Other 'Gx' Packages

amccCalculate an Adaptive Matthews Correlation Coefficient
asLongTable to data.table conversion a LongTable to a data.frame a LongTable into a 'data.table'
as.long.tableCoerce from data.table to LongTable
assayColsGeneric to access the assay columns of a rectangular object.
buildLongTableBuild a LongTable object
callingWaterfallDrug sensitivity calling using waterfall plots
cash-LongTable-methodSelect an assay from a LongTable object
cellInfocellInfo Getter
cellInfo-setcellInfo<- Generic
cellNamescellNames Generic
cellNames-setcellNames<- Generic
checkCsetStructureA function to verify the structure of a CoreSet
clevelandSmall_cSetCleaveland_mut RadioSet subsetted and cast as CoreSet
colIDsGeneric to access the row identifiers for an object.
colMetaGeneric to access the column identifiers for a rectangular...
connectivityScoreFunction computing connectivity scores between two signatures
CoreSetCoreSet constructor
CoreSet-classA Superclass to Contain Data for Genetic Profiling and...
cosinePermCosine Permutations
CreateLongTable build method from list
curationcuration Slot Getter
curation-setcuration<- Slot Setter
datasetTypedatasetType Generic
datasetType-setdatasetType<- Replacement Generic
dateCreateddateCreated Generic
dateCreated-setdateCreated<- Generic
dot-Convenience function for converting R code to a call
dot-convertCSetMolecularProfilesToSECSet molecularProfiles from ESets to SEs
dot-distancePointLineCalculate shortest distance between point and line
dot-distancePointSegmentCalculate shortest distance between point and line segment
dot-intersectListIntersect A List of More Than Two Vectors
dot-symSetDiffListUtility to find the symmetric set difference of a list of two...
dot-unionListUtility to find the union between a list of more than two...
drugSensitivitySigCompute the correlation between a molecular feature and...
featureInfofeatureInfo Generic
featureInfo-setfeatureInfo<- Generic
fNamesfNames Generic
fNames-setfNames<- Generic
getInternRetrieve the symbol for the object@.intern slot
gwcGWC Score
idColsGeneric to access the unique id columns in an S4 object used...
idCols-LongTable-methodRetrieve the unique identifier columns used for primary keys...
is.itemsGet the types of all items in a list
list_or_LongTable-classA class union to allow multiple types in a CoreSet slot
LongTableLongTable constructor method
LongTable-classLongTable class definition
mccCompute a Mathews Correlation Coefficient
mDataNamesmDataNames Generic
mDataNames-setmDataNames<- Generic
merckLongTableMerck Drug Combination Data LongTable
metadata-LongTable-methodGetter method for the metadata slot of a 'LongTable' object
metadata-set-LongTable-methodSetter method for the metadata slot of a 'LongTable' object
molecularProfilesmolecularProfiles Generic
molecularProfiles-setmolecularProfiles<- Generic
molecularProfilesSlotmolecularProfilesSlot Generic
namename Generic
name-setname<- Generic
pertNumberpertNumber Generic
pertNumber-setpertNumber<- Generic
phenoInfophenoInfo Generic
phenoInfo-setphenoInfo<- Generic
RadioSetannotation<- Slot Setter
reindexGeneric method for resetting indexing in an S4 object
reindex-LongTable-methodRedo indexing for a LongTable object to remove any gaps in...
rowIDsGeneric to access the row identifiers from
rowMetaGeneric to access the row identifiers from
sensitivityInfoGeneric function to get the annotations for a treatment...
sensitivityInfo-setsensitivityInfo<- Generic Method
sensitivityMeasuressensitivityMeasures Generic
sensitivityMeasures-setsensitivityMeasures<- Generic
sensitivityProfilessensitivityProfiles Generic
sensitivityProfiles-setsensitivityProfiles<- Generic
sensitivityRawsensitivityRaw Generic Method
sensitivityRaw-setsensitivityRaw<- Generic
sensitivitySlotsensitivitySlot Generic
sensitivitySlot-setsensitivitySlot<- Replacement Generic
sensitivitySlotToLongTablesensitivitySlotToLongTable Generic
sensNumbersensNumber Generic
sensNumber-setsensNumber<- Generic
show-CoreSet-methodShow a CoreSet
show-LongTable-methodEnsure that all rowID and colID keys are valid
showSigAnnotGet the annotations for a 'Signature' class object, as...
sub-LongTable-ANY-ANY-ANY-method[ LongTable Method
subset-LongTable-methodSubset method for a LongTable object.
subsetToSubset a CoreSet object based on various parameters, such as...
summarizeMolecularProfilesSummarize molecular profile data such that there is a single...
summarizeSensitivityProfilesSummarize across replicates for a sensitivity dose-response...
updateCellIdUpdate the cell ids in a cSet object
CoreGx documentation built on Nov. 8, 2020, 4:50 p.m.