Description Usage Arguments Value Methods (by generic) Slots Examples
A description which has yet to be added to this class. This is just a place holder.
A generic for cellInfo method
Generic for cellInfo replace method
Generic for phenoInfo method
Generic for phenoInfo replace method
Generic for molecularProfiles method
Generic for molecularProfiles replace method
Generic for featureInfo replace method
Generic for sensitivityInfo method
A generic for the sensitivityInfo replacement method
Generic for sensitivityProfiles method
A generic for the sensitivityProfiles replacement method
A generic for the sensitivityMeasures method
A generic for the cellNames method
A generic for the cellNames replacement method
A generic for the fNames method
A generic for the dateCreated method
A generic for the tSetName method
A generic for the pertNumber method
A generic for the sensNumber method
A generic for the pertNumber method
A generic for the sensNumber method
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 | ## S4 method for signature 'ToxicoSet'
cellInfo(cSet = tSet)
## S4 replacement method for signature 'ToxicoSet,data.frame'
cellInfo(object) <- value
## S4 method for signature 'ToxicoSet'
drugInfo(tSet)
## S4 replacement method for signature 'ToxicoSet,data.frame'
drugInfo(object) <- value
## S4 method for signature 'ToxicoSet,character'
phenoInfo(cSet = tSet, mDataType)
## S4 replacement method for signature 'ToxicoSet,character,data.frame'
phenoInfo(object, mDataType) <- value
## S4 method for signature 'ToxicoSet,character'
molecularProfiles(cSet = tSet, mDataType)
## S4 replacement method for signature 'ToxicoSet,character,matrix'
molecularProfiles(object, mDataType) <- value
## S4 method for signature 'ToxicoSet,character'
featureInfo(cSet = tSet, mDataType)
## S4 replacement method for signature 'ToxicoSet,character,data.frame'
featureInfo(object, mDataType) <- value
## S4 method for signature 'ToxicoSet'
sensitivityInfo(cSet = tSet)
## S4 replacement method for signature 'ToxicoSet,data.frame'
sensitivityInfo(object) <- value
## S4 method for signature 'ToxicoSet'
sensitivityProfiles(cSet = tSet)
## S4 replacement method for signature 'ToxicoSet,data.frame'
sensitivityProfiles(object) <- value
## S4 replacement method for signature 'ToxicoSet,matrix'
sensitivityProfiles(object) <- value
## S4 method for signature 'ToxicoSet'
sensitivityMeasures(cSet = tSet)
## S4 method for signature 'ToxicoSet'
drugNames(tSet)
## S4 replacement method for signature 'ToxicoSet,character'
drugNames(object) <- value
## S4 method for signature 'ToxicoSet'
cellNames(cSet = tSet)
## S4 replacement method for signature 'ToxicoSet,character'
cellNames(object) <- value
## S4 method for signature 'ToxicoSet,character'
fNames(cSet = tSet, mDataType)
## S4 method for signature 'ToxicoSet'
dateCreated(cSet = tSet)
## S4 method for signature 'ToxicoSet'
cSetName(cSet = tSet)
## S4 method for signature 'ToxicoSet'
pertNumber(cSet = tSet)
## S4 method for signature 'ToxicoSet'
sensNumber(cSet = tSet)
## S4 replacement method for signature 'ToxicoSet,array'
pertNumber(object) <- value
## S4 replacement method for signature 'ToxicoSet,matrix'
sensNumber(object) <- value
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cSet |
Parameter name for parent method inherited from CoreGx |
object |
A |
value |
A |
tSet |
A |
mDataType |
|
An object of the ToxicoSet class
a data.frame
with the cell annotations
Updated ToxicoSet
a data.frame
with the experiment info
The updated ToxicoSet
Updated ToxicoSet
Updated ToxicoSet
a data.frame
with the experiment info
Updated ToxicoSet
setGeneric("sensitivityInfo<-", function(object, value) standardGeneric("sensitivityInfo<-"))
a data.frame
with the experiment info
setGeneric("sensitivityProfiles", function(tSet) standardGeneric("sensitivityProfiles"))
Updated ToxicoSet
setGeneric("sensitivityProfiles<-", function(object, value) standardGeneric("sensitivityProfiles<-"))
A character
vector of all the available sensitivity measures
A vector of the cell names used in the ToxicoSet
Updated ToxicoSet
A character
vector of the feature names
The date the ToxicoSet was created
The name of the ToxicoSet
A 3D array
with the number of perturbation experiments per radiation type and cell line, and data type
A data.frame
with the number of sensitivity experiments per drug and cell line
The updated ToxicoSet
The updated ToxicoSet
cellInfo
: Returns the annotations for all the cell lines tested on in the ToxicoSet
cellInfo<-
: Update the cell line annotations
drugInfo
: Returns the annotations for all the drugs tested in the ToxicoSet
drugInfo<-
: Update the drug annotations
phenoInfo
: Return the experiment info from the given type of molecular data in ToxicoSet
phenoInfo<-
: Update the the given type of molecular data experiment info in the ToxicoSet
molecularProfiles
: Return the given type of molecular data from the ToxicoSet
molecularProfiles<-
: Update the given type of molecular data from the ToxicoSet
featureInfo
: Return the feature info for the given molecular data
featureInfo<-
: Replace the gene info for the molecular data
sensitivityInfo
: Return the drug dose sensitivity experiment info
sensitivityInfo<-
: Update the sensitivity experiment info
sensitivityProfiles
: Return the phenotypic data for the drug dose sensitivity
sensitivityProfiles<-
: Update the phenotypic data for the drug dose
sensitivity
sensitivityProfiles<-
: Update the phenotypic data for the drug dose
sensitivity
sensitivityMeasures
: Returns the available sensitivity profile
summaries, for example, whether there are IC50 values available
drugNames
: Return the names of the drugs used in the ToxicoSet
drugNames<-
: Update the drug names used in the dataset
cellNames
: Return the cell names used in the dataset
cellNames<-
: Update the cell names used in the dataset
fNames
: Return the feature names used in the dataset
dateCreated
: Return the date the ToxicoSet was created
cSetName
: Return the name of the ToxicoSet
pertNumber
: Return the summary of available perturbation
experiments
sensNumber
: Return the summary of available sensitivity
experiments
pertNumber<-
: Update the summary of available perturbation
experiments
sensNumber<-
: Update the summary of available sensitivity
experiments
drug
A data.frame
containg the annotations for all the drugs
profiled in the in the dataset, across all data types
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 | data(TGGATESsmall)
cellInfo <- cellInfo(TGGATESsmall)
data(TGGATESsmall)
cellInfo(TGGATESsmall) <- cellInfo(TGGATESsmall)
data(TGGATESsmall)
phenoInfo <- phenoInfo(TGGATESsmall, mDataType="rna")
data(TGGATESsmall)
phenoInfo(TGGATESsmall, mDataType="rna") <- phenoInfo(TGGATESsmall, mDataType="rna")
data(TGGATESsmall)
TGGATES_mProf <- molecularProfiles(TGGATESsmall, "rna")[1:10,]
molecularProfiles(TGGATESsmall, "rna") <- molecularProfiles(TGGATESsmall, "rna")
data(TGGATESsmall)
featureInfo <- featureInfo(TGGATESsmall, "rna")[1:10,]
data(TGGATESsmall)
featureInfo(TGGATESsmall, "rna") <- featureInfo(TGGATESsmall, "rna")
sensInf<- sensitivityInfo(TGGATESsmall)[1:10,]
data(TGGATESsmall)
sensitivityInfo(TGGATESsmall) <- sensitivityInfo(TGGATESsmall)
data(TGGATESsmall)
sensProf <- sensitivityProfiles(TGGATESsmall)
sensitivityProfiles(TGGATESsmall) <- sensitivityProfiles(TGGATESsmall)
sensitivityMeasures(TGGATESsmall)
cellNames(TGGATESsmall)
data(TGGATESsmall)
cellNames(TGGATESsmall) <- cellNames(TGGATESsmall)
fNames(TGGATESsmall, "rna")[1:10]
dateCreated(TGGATESsmall)
tSetName <- cSetName
tSetName(TGGATESsmall)
pertNumber(TGGATESsmall)
sensNumber(TGGATESsmall)
pertNumber(TGGATESsmall) <- pertNumber(TGGATESsmall)
sensNumber(TGGATESsmall) <- sensNumber(TGGATESsmall)
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