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CoreGx (version 0.1.1)

CoreSet-class: A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines

Description

The CoreSet (CSet) class was developed as a superclass for objects in the PharmacoGx and RadioGx packages to contain the data generated in screens of cancer cell lines for their genetic profile and sensitivities to therapy (Pharmacological or Radiation). This class is meant to be a superclass which is contained within the PharmacoSet (PSet) and RadioSet (RSet) objects exported by PharmacoGx and RadioGx. The format of the data is similar for both data PSets and RSets, allowing much of the code to be abstracted into the CoreSet super-class. However, the models involved with quantifying cellular response to Pharmacological and Radiation therapy are widely different, and two seperate implementations of the CSet class allows the packages to apply the correct model for the given data.

Usage

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

Arguments

cSet

A CoreSet object

object

A CoreSet object

value

A replacement value

mDataType

A character with the type of molecular data to return/update

Value

An object of the CoreSet class

Methods (by generic)

  • cellInfo: Returns the annotations for all the cell lines tested on in the CoreSet

  • cellInfo<-: Update the cell line annotations

  • phenoInfo: Return the experiment info from the given type of molecular data in CoreSet

  • phenoInfo<-: Update the the given type of molecular data experiment info in the CoreSet

  • molecularProfiles: Return the given type of molecular data from the CoreSet

  • molecularProfiles<-: Update the given type of molecular data from the CoreSet

  • 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

  • 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 CoreSet was created

  • cSetName: Return the name of the CoreSet

  • 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

annotation

A list of annotation data about the CoreSet, including the $name and the session information for how the object was creating, detailing the exact versions of R and all the packages used

molecularProfiles

A list containing 4 Biobase::ExpressionSet type object for holding data for RNA, DNA, SNP and Copy Number Variation measurements respectively, with associated fData and pData containing the row and column metadata

cell

A data.frame containg the annotations for all the cell lines profiled in the data set, across all data types

sensitivity

A list containing all the data for the sensitivity experiments, including $info, a data.frame containing the experimental info,$raw a 3D array containing raw data, $profiles, a data.frame containing sensitivity profiles statistics, and $n, a data.frame detailing the number of experiments for each cell-drug/radiationInfo pair

perturbation

A list containting $n, a data.frame summarizing the available perturbation data,

curation

A list containing mappings for cell, tissue names used in the data set to universal identifiers used between different CoreSet objects

datasetType

A character string of 'sensitivity', 'perturbation', or both detailing what type of data can be found in the CoreSet, for proper processing of the data