RadioGx (version 0.0.2)

RadioSet-class: A Class to Contain RadioGenomic datasets together with their curations

Description

The RadioSet (RSet) class was developed to contain and organise large RadioGenomic datasets, and aid in their metanalysis. It was designed primarily to allow bioinformaticians and biologists to work with data at the level of genes and cell lines, providing a more naturally intuitive interface and simplifying analyses between several datasets. As such, it was designed to be flexible enough to hold datasets of two different natures while providing a common interface. The class can accomidate datasets containing both radiation dose response data, as well as datasets contaning genetic profiles of cell lines pre and post treatement with compounds, known respecitively as sensitivity and perturbation datasets.

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

Arguments

cSet

Parameter name for parent method inherited from CoreGx

object

A RadioSet object

value

A replacement value

rSet

A RadioSet object

mDataType

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

Value

An object of the RadioSet class

a data.frame with the cell annotations

Updated RadioSet

a data.frame with the experiment info

The updated RadioSet

a data.frame with the experiment info

Updated RadioSet

Updated RadioSet

a data.frame with the experiment info

Updated RadioSet

a data.frame with the experiment info

Updated RadioSet

A character vector of all the available sensitivity measures

A vector of the cell names used in the RadioSet

Updated RadioSet

A character vector of the feature names

The date the RadioSet was created

The name of the RadioSet

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 radiation type and cell line

The updated RadioSet

The updated RadioSet

Methods (by generic)

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

• cellInfo<-: Update the cell line annotations

• radiationInfo: Returns the annotations for all the radiations tested in the RadioSet

• radiationInfo<-: Update the radiation annotations

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

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

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

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

• featureInfo: Return the feature info for the given molecular data

• featureInfo<-: Replace the gene info for the molecular data

• sensitivityInfo: Return the radiation dose sensitivity experiment info

• sensitivityInfo<-: Update the sensitivity experiment info

• sensitivityProfiles: Return the phenotypic data for the radiation dose sensitivity

• sensitivityProfiles<-: Update the phenotypic data for the radiation dose sensitivity

• sensitivityProfiles<-: Update the phenotypic data for the radiation dose sensitivity

• sensitivityMeasures: Returns the available sensitivity profile summaries, for example, whether there are IC50 values available

• radiationTypes: Return the names of the radiations used in the RadioSet

• radiationTypes<-: Update the radiation 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 RadioSet was created

• cSetName: Return the name of the RadioSet

• 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 RadioSet, 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

radiation

A data.frame containg the annotations for all the radiation treatment types used in the in the dataset, 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-radiation type pair

perturbation

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

curation

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

datasetType

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

Examples

# NOT RUN {
phenoInfo(Cleveland_small, mDataType="rna")


phenoInfo(Cleveland_small, mDataType="rna") <- phenoInfo(Cleveland_small, mDataType="rna")

Cleveland_mProf <- molecularProfiles(Cleveland_small, "rna")
Cleveland_mProf[1:10,]

molecularProfiles(Cleveland_small, "rna") <- molecularProfiles(Cleveland_small, "rna")

featureInfo(Cleveland_small, "rna")[1:10,]

featureInfo(Cleveland_small, "rna") <- featureInfo(Cleveland_small, "rna")

sensInf<- sensitivityInfo(Cleveland_small)
sensInf[1:10,]

sensitivityInfo(Cleveland_small) <- sensitivityInfo(Cleveland_small)

sensitivityProfiles(Cleveland_small)

sensitivityProfiles(Cleveland_small) <- sensitivityProfiles(Cleveland_small)

sensitivityMeasures(Cleveland_small)


cellNames(Cleveland_small)

cellNames(Cleveland_small) <- cellNames(Cleveland_small)

fNames(Cleveland_small, "rna")[1:10]

dateCreated(Cleveland_small)

rSetName <- cSetName
rSetName(Cleveland_small)

pertNumber(Cleveland_small)

sensNumber(Cleveland_small)

pertNumber(Cleveland_small) <- pertNumber(Cleveland_small)

sensNumber(Cleveland_small) <- sensNumber(Cleveland_small)

# }