A B C D E F G I L M N O P R S T U misc
amcc | Calculate an Adaptive Matthews Correlation Coefficient |
annotation | Accessing and modifying information in a 'CoreSet' |
annotation-method | Accessing and modifying information in a 'CoreSet' |
annotation<- | Accessing and modifying information in a 'CoreSet' |
annotation<--method | Accessing and modifying information in a 'CoreSet' |
as | LongTable to data.table conversion |
as.data.frame.long.table | LongTable to data.table conversion |
as.data.table.long.table | LongTable to data.table conversion |
as.long.table | Coerce from data.table to LongTable |
assayCols | Generic to access the assay columns of a rectangular object. |
assayMap | Accessing and modifying data in a 'LongTableDataMapper' object. |
assayMap-method | Accessing and modifying data in a 'LongTableDataMapper' object. |
assayMap<- | Accessing and modifying data in a 'LongTableDataMapper' object. |
assayMap<-,LongTableDataMapper,List-methhod | Accessing and modifying data in a 'LongTableDataMapper' object. |
assayMap<--method | Accessing and modifying data in a 'LongTableDataMapper' object. |
assignment-immutable | Intercept assignment operations for "immutable" S3 objects. |
buildLongTable | Build a LongTable object |
buildLongTable-method | LongTable build method from character |
buildLongTable-method | LongTable build method |
buildLongTable-method | LongTable build method from list |
c.immutable | Intercept concatenation for "immutable" class objects to return another "immutable" class object. |
cardinality | Search a data.frame for 1:'cardinality' relationships between a group of columns (your identifiers) and all other columns. |
cellInfo | Accessing and modifying information in a 'CoreSet' |
cellInfo-method | Accessing and modifying information in a 'CoreSet' |
cellInfo<- | Accessing and modifying information in a 'CoreSet' |
cellInfo<--method | Accessing and modifying information in a 'CoreSet' |
cellName-method | Accessing and modifying information in a 'CoreSet' |
cellNames | Accessing and modifying information in a 'CoreSet' |
cellNames<- | Accessing and modifying information in a 'CoreSet' |
cellNames<--method | Accessing and modifying information in a 'CoreSet' |
checkColumnCardinality | Search a data.frame for 1:'cardinality' relationships between a group of columns (your identifiers) and all other columns. |
checkCsetStructure | A function to verify the structure of a CoreSet |
clevelandSmall_cSet | Cleaveland_mut RadioSet subsetted and cast as CoreSet |
colData-method | Convenience method to subset the 'colData' out of the 'rawdata' slot using the assigned 'colDataMap' metadata. |
colDataMap | Accessing and modifying data in a 'LongTableDataMapper' object. |
colDataMap-method | Accessing and modifying data in a 'LongTableDataMapper' object. |
colDataMap<- | Accessing and modifying data in a 'LongTableDataMapper' object. |
colDataMap<--method | Accessing and modifying data in a 'LongTableDataMapper' object. |
colDataMap<-LongTableDataMapper-method | Accessing and modifying data in a 'LongTableDataMapper' object. |
colIDs | Generic to access the row identifiers for an object. |
colMeta | Generic to access the column identifiers for a rectangular object. |
colnames<- | Intercept assignment operations for "immutable" S3 objects. |
colnames<-, | Intercept assignment operations for "immutable" S3 objects. |
colnames<-.immutable | Intercept assignment operations for "immutable" S3 objects. |
connectivityScore | Function computing connectivity scores between two signatures |
CoreGx-defunct | List of 'deprecated' or 'defunct' methods in the 'CoreGx' R package. |
CoreGx-deprecated | List of 'deprecated' or 'defunct' methods in the 'CoreGx' R package. |
CoreSet | CoreSet constructor |
CoreSet-accessors | Accessing and modifying information in a 'CoreSet' |
CoreSet-class | CoreSet - A generic data container for molecular profiles and treatment response data |
CoreSet-utils | Utility methods for a 'CoreSet' object. |
CoreSet2 | Make a CoreSet with the updated class structure |
cosinePerm | Cosine Permutations |
curation | Accessing and modifying information in a 'CoreSet' |
curation-method | Accessing and modifying information in a 'CoreSet' |
curation<- | Accessing and modifying information in a 'CoreSet' |
curation<--method | Accessing and modifying information in a 'CoreSet' |
DataMapper-accessors | Accessing and modifying data in a 'DataMapper' object. |
DataMapper-class | An S4 Class For Mapping from Raw Experimental Data to a Specific S4 Object |
datasetType | Accessing and modifying information in a 'CoreSet' |
datasetType-method | Accessing and modifying information in a 'CoreSet' |
datasetType<- | Accessing and modifying information in a 'CoreSet' |
datasetType<--method | Accessing and modifying information in a 'CoreSet' |
dateCreated | Accessing and modifying information in a 'CoreSet' |
dateCreated-method | Accessing and modifying information in a 'CoreSet' |
dateCreated<- | Accessing and modifying information in a 'CoreSet' |
dateCreated<--method | Accessing and modifying information in a 'CoreSet' |
dimnames<- | Intercept assignment operations for "immutable" S3 objects. |
dimnames<-, | Intercept assignment operations for "immutable" S3 objects. |
dimnames<-.immutable | Intercept assignment operations for "immutable" S3 objects. |
exampleDataMapper | Example LongTableDataMapper |
featureInfo | Accessing and modifying information in a 'CoreSet' |
featureInfo-method | Accessing and modifying information in a 'CoreSet' |
featureInfo<- | Accessing and modifying information in a 'CoreSet' |
featureInfo<--method | Accessing and modifying information in a 'CoreSet' |
fNames | Accessing and modifying information in a 'CoreSet' |
fNames-method | Accessing and modifying information in a 'CoreSet' |
fNames<- | Accessing and modifying information in a 'CoreSet' |
fNames<--method | Accessing and modifying information in a 'CoreSet' |
getIntern | Retrieve the specified item from object internal metadata. |
guessMapping | Generic for Guessing the Mapping Between Some Raw Data and an S4 Object |
guessMapping-method | Guess which columns in raw experiment data map to which dimensions. |
gwc | GWC Score |
idCols | Generic to access the unique id columns in an S4 object used to |
idCols-method | Retrieve the unique identifier columns used for primary keys in rowData and colData. |
immutable | Constructor for "immutable" S3-class property |
immutable_list-class | Constructor for "immutable" S3-class property |
is.immutable | Check if an R object inherits from the immutable S3-class. |
is.items | Get the types of all items in a list |
lapply-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' |
LongTableDataMapper | Constructor for the 'LongTableDataMapper' class, which maps from one or more raw experimental data files to the slots of a 'LongTable' object. |
LongTableDataMapper-accessors | Accessing and modifying data in a 'LongTableDataMapper' object. |
LongTableDataMapper-class | A Class for Mapping Between Raw Data and an 'LongTable' Object |
mcc | Compute a Mathews Correlation Coefficient |
mDataNames | Accessing and modifying information in a 'CoreSet' |
mDataNames-method | Accessing and modifying information in a 'CoreSet' |
mDataNames<- | Accessing and modifying information in a 'CoreSet' |
mDataNames<--method | Accessing and modifying information in a 'CoreSet' |
merckLongTable | Merck Drug Combination Data LongTable |
metaConstruct | Generic for preprocessing complex data before being used in the constructor of an 'S4' container object. |
metaConstruct-method | Generic for preprocessing complex data before being used in the constructor of an 'S4' container object. |
metadata-method | Getter method for the metadata slot of a 'LongTable' object |
metadata<--method | Setter method for the metadata slot of a 'LongTable' object |
metadataMap | Accessing and modifying data in a 'LongTableDataMapper' object. |
metadataMap-method | Accessing and modifying data in a 'LongTableDataMapper' object. |
metadataMap<- | Accessing and modifying data in a 'LongTableDataMapper' object. |
metadataMap<--method | Accessing and modifying data in a 'LongTableDataMapper' object. |
molecularProfiles | Accessing and modifying information in a 'CoreSet' |
molecularProfiles-method | Accessing and modifying information in a 'CoreSet' |
molecularProfiles<- | Accessing and modifying information in a 'CoreSet' |
molecularProfiles<--method | Accessing and modifying information in a 'CoreSet' |
molecularProfilesSlot | Accessing and modifying information in a 'CoreSet' |
molecularProfilesSlot-method | Accessing and modifying information in a 'CoreSet' |
molecularProfilesSlot<- | Accessing and modifying information in a 'CoreSet' |
molecularProfilesSlot<--method | Accessing and modifying information in a 'CoreSet' |
molecularProfilesSlot<-CoreSet-method | Accessing and modifying information in a 'CoreSet' |
moleculerProfilesSlot-method | Accessing and modifying information in a 'CoreSet' |
mutable | Remove the "immutable" S3-class from an R object, allowing it to be modified normally again. |
name | Accessing and modifying information in a 'CoreSet' |
name-method | Accessing and modifying information in a 'CoreSet' |
name<- | Accessing and modifying information in a 'CoreSet' |
name<--method | Accessing and modifying information in a 'CoreSet' |
names<- | Intercept assignment operations for "immutable" S3 objects. |
names<-.immutable | Intercept assignment operations for "immutable" S3 objects. |
optimizeCoreGx | A helper method to find the best multithreading configuration for your computer |
pertNumber | Accessing and modifying information in a 'CoreSet' |
pertNumber-method | Accessing and modifying information in a 'CoreSet' |
pertNumber<- | Accessing and modifying information in a 'CoreSet' |
pertNumber<--method | Accessing and modifying information in a 'CoreSet' |
phenoInfo | Accessing and modifying information in a 'CoreSet' |
phenoInfo-method | Accessing and modifying information in a 'CoreSet' |
phenoInfo<- | Accessing and modifying information in a 'CoreSet' |
phenoInfo<--method | Accessing and modifying information in a 'CoreSet' |
print.immutable | Print method for objects inheriting from the "immutable" S3-class |
rawdata | Accessing and modifying data in a 'DataMapper' object. |
rawdata-method | Accessing and modifying data in a 'DataMapper' object. |
rawdata-method | Accessing and modifying data in a 'LongTableDataMapper' object. |
rawdata<- | Accessing and modifying data in a 'DataMapper' object. |
rawdata<--method | Accessing and modifying data in a 'DataMapper' object. |
rawdata<--method | Accessing and modifying data in a 'LongTableDataMapper' object. |
reindex | Generic method for resetting indexing in an S4 object |
reindex-method | Redo indexing for a LongTable object to remove any gaps in integer indexes |
rowData-method | Convenience method to subset the 'rowData' out of the 'rawdata' slot using the assigned 'rowDataMap' metadata. |
rowDataMap | Accessing and modifying data in a 'LongTableDataMapper' object. |
rowDataMap-method | Accessing and modifying data in a 'LongTableDataMapper' object. |
rowDataMap<- | Accessing and modifying data in a 'LongTableDataMapper' object. |
rowDataMap<--method | Accessing and modifying data in a 'LongTableDataMapper' object. |
rowDataMap<-LongTableDataMapper-method | Accessing and modifying data in a 'LongTableDataMapper' object. |
rowIDs | Generic to access the row identifiers from |
rowMeta | Generic to access the row identifiers from |
rownames<- | Intercept assignment operations for "immutable" S3 objects. |
rownames<-, | Intercept assignment operations for "immutable" S3 objects. |
rownames<-.immutable | Intercept assignment operations for "immutable" S3 objects. |
sampleInfo | Accessing and modifying information in a 'CoreSet' |
sampleInfo-method | Accessing and modifying information in a 'CoreSet' |
sampleInfo<- | Accessing and modifying information in a 'CoreSet' |
sampleInfo<--method | Accessing and modifying information in a 'CoreSet' |
sampleName-method | Accessing and modifying information in a 'CoreSet' |
sampleNames | Accessing and modifying information in a 'CoreSet' |
sampleNames-method | Accessing and modifying information in a 'CoreSet' |
sampleNames<- | Accessing and modifying information in a 'CoreSet' |
sampleNames<--method | Accessing and modifying information in a 'CoreSet' |
sensitivityInfo | Generic function to get the annotations for a treatment response experiment from an S4 class |
sensitivityInfo-method | Accessing and modifying information in a 'CoreSet' |
sensitivityInfo<- | sensitivityInfo<- Generic Method |
sensitivityInfo<--method | Accessing and modifying information in a 'CoreSet' |
sensitivityMeasures | sensitivityMeasures Generic |
sensitivityMeasures-method | Accessing and modifying information in a 'CoreSet' |
sensitivityMeasures<- | sensitivityMeasures<- Generic |
sensitivityMeasures<--method | Accessing and modifying information in a 'CoreSet' |
sensitivityProfiles | sensitivityProfiles Generic |
sensitivityProfiles-method | Accessing and modifying information in a 'CoreSet' |
sensitivityProfiles<- | sensitivityProfiles<- Generic |
sensitivityProfiles<--method | Accessing and modifying information in a 'CoreSet' |
sensitivityRaw | sensitivityRaw Generic Method |
sensitivityRaw-method | Accessing and modifying information in a 'CoreSet' |
sensitivityRaw<- | sensitivityRaw<- Generic |
sensitivityRaw<--method | Accessing and modifying information in a 'CoreSet' |
sensitivitySlot | Accessing and modifying information in a 'CoreSet' |
sensitivitySlot-method | Accessing and modifying information in a 'CoreSet' |
sensitivitySlot<- | Accessing and modifying information in a 'CoreSet' |
sensitivitySlot<--method | Accessing and modifying information in a 'CoreSet' |
sensitivitySlotToLongTable | sensitivitySlotToLongTable Generic |
sensitvityInfo<--method | Accessing and modifying information in a 'CoreSet' |
sensNumber | Accessing and modifying information in a 'CoreSet' |
sensNumber-method | Accessing and modifying information in a 'CoreSet' |
sensNumber<- | Accessing and modifying information in a 'CoreSet' |
sensNumber<--method | Accessing and modifying information in a 'CoreSet' |
setOps-immutable | Subset an immutable object, returning another immutable object. |
show-method | A Class for Mapping Between Raw Data and an 'LongTable' Object |
show-method | Show a CoreSet |
show-method | Show method for the LongTable class |
show.immutable | Constructor for "immutable" S3-class property |
showSigAnnot | Get the annotations for a 'Signature' class object, as returned by 'drugSensitivitysig' or 'radSensitivtySig' functions available in 'PharmacoGx' and 'RadioGx', respectively. |
subset, | Subset an immutable object, returning another immutable object. |
subset-method | Subset method for a LongTable object. |
subset.immutable | Subset an immutable object, returning another immutable object. |
subset<-, | Intercept assignment operations for "immutable" S3 objects. |
subset<-.immutable | Intercept assignment operations for "immutable" S3 objects. |
subsetByFeature | Utility methods for a 'CoreSet' object. |
subsetByFeature-method | Utility methods for a 'CoreSet' object. |
subsetBySample | Utility methods for a 'CoreSet' object. |
subsetBySample-method | Utility methods for a 'CoreSet' object. |
subsetByTreatment | Utility methods for a 'CoreSet' object. |
subsetByTreatment-method | Utility methods for a 'CoreSet' object. |
summarizeMolecularProfiles | Summarize molecular profile data such that there is a single entry for each sample line/treatment combination |
summarizeSensitivityProfiles | Summarize across replicates for a sensitivity dose-response experiment |
treatmentInfo | Accessing and modifying information in a 'CoreSet' |
treatmentInfo-method | Accessing and modifying information in a 'CoreSet' |
treatmentInfo<- | Accessing and modifying information in a 'CoreSet' |
treatmentInfo<--method | Accessing and modifying information in a 'CoreSet' |
treatmentNames | Accessing and modifying information in a 'CoreSet' |
treatmentNames-method | Accessing and modifying information in a 'CoreSet' |
treatmentNames<- | Accessing and modifying information in a 'CoreSet' |
treatmentNames<--method | Accessing and modifying information in a 'CoreSet' |
TreatmentResponseExperiment | TreatmentResponseExperiment constructor method |
TREDataMapper | Constructor for the 'TREDataMapper' class, which maps from one or more raw experimental data files to the slots of a 'LongTable' object. |
TREDataMapper-class | A Class for Mapping Between Raw Data and an 'TreatmentResponseExperiment' Object |
updateObject-method | Update the 'CoreSet' class after changes in it struture or API |
updateObject-method | Update the 'LongTable' class after changes in it struture or API |
$ | Subset an immutable object, returning another immutable object. |
$-method | Select an assay from a LongTable object |
$.immutable | Subset an immutable object, returning another immutable object. |
$<- | Intercept assignment operations for "immutable" S3 objects. |
$<-, | Intercept assignment operations for "immutable" S3 objects. |
$<--method | Update an assay from a LongTable object |
$<-.immutable | Intercept assignment operations for "immutable" S3 objects. |
. | Convenience function for converting R code to a call |
.assayToBumpyMatrix | Convert a LongTable assay into a BumpyMatrix object |
.CoreSet | CoreSet - A generic data container for molecular profiles and treatment response data |
.DataMapper | An S4 Class For Mapping from Raw Experimental Data to a Specific S4 Object |
.LongTableDataMapper | A Class for Mapping Between Raw Data and an 'LongTable' Object |
.longTableToSummarizedExperiment | Convert LongTable to gDR Style SummarizedExperiment |
.TREDataMapper | A Class for Mapping Between Raw Data and an 'TreatmentResponseExperiment' Object |
[ | Subset an immutable object, returning another immutable object. |
[, | Subset an immutable object, returning another immutable object. |
[-method | [ LongTable Method |
[.immutable | Subset an immutable object, returning another immutable object. |
[<- | Intercept assignment operations for "immutable" S3 objects. |
[<-, | Intercept assignment operations for "immutable" S3 objects. |
[<-.immutable | Intercept assignment operations for "immutable" S3 objects. |
[[ | Subset an immutable object, returning another immutable object. |
[[, | Subset an immutable object, returning another immutable object. |
[[.immutable | Subset an immutable object, returning another immutable object. |
[[<- | Intercept assignment operations for "immutable" S3 objects. |
[[<-, | Intercept assignment operations for "immutable" S3 objects. |
[[<--method | [[<- Method for LongTable Class |
[[<-.immutable | Intercept assignment operations for "immutable" S3 objects. |