ToxicoGx (version 0.1.1)

ToxicoSet-class: Class to contain Toxico-genomic Data

Description

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

Usage

# S4 method for ToxicoSet
cellInfo(cSet = tSet)
# S4 method for ToxicoSet,data.frame
cellInfo(object) <- value
# S4 method for ToxicoSet
drugInfo(tSet)
# S4 method for ToxicoSet,data.frame
drugInfo(object) <- value
# S4 method for ToxicoSet,character
phenoInfo(cSet = tSet, mDataType)
# S4 method for ToxicoSet,character,data.frame
phenoInfo(object, mDataType) <- value
# S4 method for ToxicoSet,character
molecularProfiles(cSet = tSet, mDataType)
# S4 method for ToxicoSet,character,matrix
molecularProfiles(object, mDataType) <- value
# S4 method for ToxicoSet,character
featureInfo(cSet = tSet, mDataType)
# S4 method for ToxicoSet,character,data.frame
featureInfo(object, mDataType) <- value
# S4 method for ToxicoSet
sensitivityInfo(cSet = tSet)
# S4 method for ToxicoSet,data.frame
sensitivityInfo(object) <- value
# S4 method for ToxicoSet
sensitivityProfiles(cSet = tSet)
# S4 method for ToxicoSet,data.frame
sensitivityProfiles(object) <- value
# S4 method for ToxicoSet,matrix
sensitivityProfiles(object) <- value
# S4 method for ToxicoSet
sensitivityMeasures(cSet = tSet)
# S4 method for ToxicoSet
drugNames(tSet)
# S4 method for ToxicoSet,character
drugNames(object) <- value
# S4 method for ToxicoSet
cellNames(cSet = tSet)
# S4 method for ToxicoSet,character
cellNames(object) <- value
# S4 method for ToxicoSet,character
fNames(cSet = tSet, mDataType)
# S4 method for ToxicoSet
dateCreated(cSet = tSet)
# S4 method for ToxicoSet
cSetName(cSet = tSet)
# S4 method for ToxicoSet
pertNumber(cSet = tSet)
# S4 method for ToxicoSet
sensNumber(cSet = tSet)
# S4 method for ToxicoSet,array
pertNumber(object) <- value
# S4 method for ToxicoSet,matrix
sensNumber(object) <- value

Arguments

cSet

Parameter name for parent method inherited from CoreGx

object

A ToxicoSet object to modify

value

A matrix of replacement values

tSet

A ToxicoSet object

mDataType

character A string specifying the type of molecular data to list the phenotype information for.

Value

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

Methods (by generic)

• 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

Slots

drug

A data.frame containg the annotations for all the drugs profiled in the in the dataset, across all data types

Examples

# NOT RUN {
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)

# }