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CoreSet-class: A Superclass to Contain Data for Genetic Profiling and...

CoreSet-class: A Superclass to Contain Data for Genetic Profiling and...
In CoreGx: Classes and Functions to Serve as the Basis for Other 'Gx' Packages

Description Usage Arguments Value Methods (by generic) Slots Examples

Description

The CoreSet (CSet) class was developed as a superclass for pSets 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 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 extension of the cSet class allows the packages to apply the correct model for the given data.

Generic for sensitivityInfo method

A generic for the sensitivityInfo replacement method

Usage

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## S4 method for signature 'CoreSet'
annotation(object)

## S4 method for signature 'CoreSet'
cellInfo(object)

## S4 replacement method for signature 'CoreSet,data.frame'
cellInfo(object) <- value

## S4 method for signature 'CoreSet'
cellNames(object)

## S4 replacement method for signature 'CoreSet,character'
cellNames(object) <- value

## S4 method for signature 'CoreSet'
curation(object)

## S4 replacement method for signature 'CoreSet,list'
curation(object) <- value

## S4 method for signature 'CoreSet'
datasetType(object)

## S4 replacement method for signature 'CoreSet'
datasetType(object) <- value

## S4 method for signature 'CoreSet'
dateCreated(object)

## S4 replacement method for signature 'CoreSet'
dateCreated(object) <- value

## S4 method for signature 'CoreSet'
fNames(object, mDataType)

## S4 replacement method for signature 'CoreSet,character,character'
fNames(object, mDataType) <- value

## S4 method for signature 'CoreSet'
featureInfo(object, mDataType)

## S4 replacement method for signature 'CoreSet,character,data.frame'
featureInfo(object, mDataType) <- value

## S4 replacement method for signature 'CoreSet,character,DataFrame'
featureInfo(object, mDataType) <- value

## S4 method for signature 'CoreSet'
mDataNames(object)

## S4 replacement method for signature 'CoreSet'
mDataNames(object) <- value

## S4 method for signature 'CoreSet'
molecularProfiles(object, mDataType, assay)

## S4 replacement method for signature 'CoreSet,character,character,matrix'
molecularProfiles(object, mDataType, assay) <- value

## S4 replacement method for signature 'CoreSet,character,missing,matrix'
molecularProfiles(object, mDataType, assay) <- value

## S4 method for signature 'CoreSet'
molecularProfilesSlot(object)

## S4 replacement method for signature 'CoreSet,list'
molecularProfilesSlot(object) <- value

## S4 method for signature 'CoreSet'
name(object)

## S4 replacement method for signature 'CoreSet'
name(object) <- value

## S4 method for signature 'CoreSet'
pertNumber(object)

## S4 replacement method for signature 'CoreSet,array'
pertNumber(object) <- value

## S4 method for signature 'CoreSet'
phenoInfo(object, mDataType)

## S4 replacement method for signature 'CoreSet,character,data.frame'
phenoInfo(object, mDataType) <- value

## S4 replacement method for signature 'CoreSet,character,DataFrame'
phenoInfo(object, mDataType) <- value

## S4 method for signature 'CoreSet'
sensNumber(object)

## S4 replacement method for signature 'CoreSet,matrix'
sensNumber(object) <- value

## S4 method for signature 'CoreSet'
sensitivityInfo(object)

## S4 replacement method for signature 'CoreSet,data.frame'
sensitivityInfo(object) <- value

## S4 method for signature 'CoreSet'
sensitivityMeasures(object)

## S4 replacement method for signature 'CoreSet,character'
sensitivityMeasures(object) <- value

## S4 method for signature 'CoreSet'
sensitivityProfiles(object)

## S4 replacement method for signature 'CoreSet,data.frame'
sensitivityProfiles(object) <- value

## S4 replacement method for signature 'CoreSet,matrix'
sensitivityProfiles(object) <- value

## S4 method for signature 'CoreSet'
sensitivityRaw(object)

## S4 replacement method for signature 'CoreSet,array'
sensitivityRaw(object) <- value

## S4 method for signature 'CoreSet'
sensitivitySlot(object)

## S4 replacement method for signature 'CoreSet,list'
sensitivitySlot(object) <- value

Arguments

object

An ['CoreSet'] to extract the raw sensitivity data from.

value

A 3D ['array'] containing the raw dose and viability measurements to update the object with.

mDataType

character The type of molecular data

assay

character Name of the desired assay; if excluded defaults to first assay in the SummarizedExperiment for the given mDataType. Use assayNames(molecularProfiles(object, dataType) to check which assays are available for a given molecular datatype.

Value

An object of the CoreSet class

A list of named annotaiton

A list of unique cell and tissue identifiers to check validity of a cSet

A copy of the RadioSet with the updated curation slot

a data.frame with the experiment info if dimension is excluded, otherwise a 'data.table' with annotations for the cells or drugs dimension of the LongTable.

Updated CoreSet

A ['character'] vector of all the available sensitivity measures.

A update CoreSet object with the new sensitivity measures

a ['data.frame'] with sensitivity profile summaries for CoreSet

Updated CoreSet

A ['array'] containing the raw sensitivity data as experiment by dose level by metric.

A 3D ['array'] containing the raw sensitivity data as experiment by dose level by metric.

Methods (by generic)

Slots

annotation

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

molecularProfiles

A list containing SummarizedExperiments type object for holding data for RNA, DNA, SNP and Copy Number Variation measurements respectively, with associated rowData and colData 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

Examples

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annotation(clevelandSmall_cSet)

data(clevelandSmall_cSet)
curation(clevelandSmall_cSet)

data(clevelandSmall_cSet)
curation(clevelandSmall_cSet) <- curation(clevelandSmall_cSet)

data(clevelandSmall_cSet)
sensitivityInfo(clevelandSmall_cSet)

sensitivityInfo(clevelandSmall_cSet) <- sensitivityInfo(clevelandSmall_cSet)

sensitivityMeasures(clevelandSmall_cSet)

data(clevelandSmall_cSet)
sensitivityMeasures(clevelandSmall_cSet) <- sensitivityMeasures(clevelandSmall_cSet)

sensitivityProfiles(clevelandSmall_cSet)

sensitivityProfiles(clevelandSmall_cSet) <- sensitivityProfiles(clevelandSmall_cSet)

data(clevelandSmall_cSet)
sensRaw <- sensitivityRaw(clevelandSmall_cSet)
head(sensRaw)

data(clevelandSmall_cSet)
sensitivityRaw(clevelandSmall_cSet) <- sensitivityRaw(clevelandSmall_cSet)

CoreGx documentation built on Nov. 8, 2020, 4:50 p.m.

Related to CoreSet-class in CoreGx...

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CoreGx: Class and Function Abstractions for PharmacoGx, RadioGx and ToxicoGx The LongTable Class

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