RadioSet-class: A Class to Contain RadioGenomic datasets together with their...
In RadioGx: Analysis of Large-Scale Radio-Genomic Data
Description
Usage
Arguments
Value
Methods (by generic)
Slots
Examples
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
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## S4 method for signature 'RadioSet'
cellInfo(cSet = rSet)
## S4 replacement method for signature 'RadioSet,data.frame'
cellInfo(object) <- value
## S4 method for signature 'RadioSet'
radiationInfo(rSet)
## S4 replacement method for signature 'RadioSet,data.frame'
radiationInfo(object) <- value
## S4 method for signature 'RadioSet,character'
phenoInfo(cSet = rSet, mDataType)
## S4 replacement method for signature 'RadioSet,character,data.frame'
phenoInfo(object,
mDataType) <- value
## S4 method for signature 'RadioSet,character'
molecularProfiles(cSet = rSet, mDataType)
## S4 replacement method for signature 'RadioSet,character,matrix'
molecularProfiles(object,
mDataType) <- value
## S4 method for signature 'RadioSet,character'
featureInfo(cSet = rSet, mDataType)
## S4 replacement method for signature 'RadioSet,character,data.frame'
featureInfo(object,
mDataType) <- value
## S4 method for signature 'RadioSet'
sensitivityInfo(cSet = rSet)
## S4 replacement method for signature 'RadioSet,data.frame'
sensitivityInfo(object) <- value
## S4 method for signature 'RadioSet'
sensitivityProfiles(cSet = rSet)
## S4 replacement method for signature 'RadioSet,data.frame'
sensitivityProfiles(object) <- value
## S4 replacement method for signature 'RadioSet,matrix'
sensitivityProfiles(object) <- value
## S4 method for signature 'RadioSet'
sensitivityMeasures(cSet = rSet)
## S4 method for signature 'RadioSet'
radiationTypes(rSet)
## S4 replacement method for signature 'RadioSet,character'
radiationTypes(object) <- value
## S4 method for signature 'RadioSet'
cellNames(cSet = rSet)
## S4 replacement method for signature 'RadioSet,character'
cellNames(object) <- value
## S4 method for signature 'RadioSet,character'
fNames(cSet = rSet, mDataType)
## S4 method for signature 'RadioSet'
dateCreated(cSet = rSet)
## S4 method for signature 'RadioSet'
cSetName(cSet = rSet)
## S4 method for signature 'RadioSet'
pertNumber(cSet = rSet)
## S4 method for signature 'RadioSet'
sensNumber(cSet = rSet)
## S4 replacement method for signature 'RadioSet,array'
pertNumber(object) <- value
## S4 replacement method for signature '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
annotationA 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
molecularProfilesA 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
cellA data.frame containg the annotations for all the cell
lines profiled in the data set, across all data types
radiationA data.frame containg the annotations for all the radiation treatment types
used in the in the dataset, across all data types
sensitivityA 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
perturbationA list containting $n, a data.frame
summarizing the available perturbation data,
curationA list containing mappings for
cell and tissue names used in the data set to universal
identifiers used between different RadioSet objects
datasetTypeA 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
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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)
RadioGx documentation built on Dec. 20, 2019, 1:06 a.m.
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Description Usage Arguments Value Methods (by generic) Slots Examples
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
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 81 82 83 | ## S4 method for signature 'RadioSet'
cellInfo(cSet = rSet)
## S4 replacement method for signature 'RadioSet,data.frame'
cellInfo(object) <- value
## S4 method for signature 'RadioSet'
radiationInfo(rSet)
## S4 replacement method for signature 'RadioSet,data.frame'
radiationInfo(object) <- value
## S4 method for signature 'RadioSet,character'
phenoInfo(cSet = rSet, mDataType)
## S4 replacement method for signature 'RadioSet,character,data.frame'
phenoInfo(object,
mDataType) <- value
## S4 method for signature 'RadioSet,character'
molecularProfiles(cSet = rSet, mDataType)
## S4 replacement method for signature 'RadioSet,character,matrix'
molecularProfiles(object,
mDataType) <- value
## S4 method for signature 'RadioSet,character'
featureInfo(cSet = rSet, mDataType)
## S4 replacement method for signature 'RadioSet,character,data.frame'
featureInfo(object,
mDataType) <- value
## S4 method for signature 'RadioSet'
sensitivityInfo(cSet = rSet)
## S4 replacement method for signature 'RadioSet,data.frame'
sensitivityInfo(object) <- value
## S4 method for signature 'RadioSet'
sensitivityProfiles(cSet = rSet)
## S4 replacement method for signature 'RadioSet,data.frame'
sensitivityProfiles(object) <- value
## S4 replacement method for signature 'RadioSet,matrix'
sensitivityProfiles(object) <- value
## S4 method for signature 'RadioSet'
sensitivityMeasures(cSet = rSet)
## S4 method for signature 'RadioSet'
radiationTypes(rSet)
## S4 replacement method for signature 'RadioSet,character'
radiationTypes(object) <- value
## S4 method for signature 'RadioSet'
cellNames(cSet = rSet)
## S4 replacement method for signature 'RadioSet,character'
cellNames(object) <- value
## S4 method for signature 'RadioSet,character'
fNames(cSet = rSet, mDataType)
## S4 method for signature 'RadioSet'
dateCreated(cSet = rSet)
## S4 method for signature 'RadioSet'
cSetName(cSet = rSet)
## S4 method for signature 'RadioSet'
pertNumber(cSet = rSet)
## S4 method for signature 'RadioSet'
sensNumber(cSet = rSet)
## S4 replacement method for signature 'RadioSet,array'
pertNumber(object) <- value
## S4 replacement method for signature 'RadioSet,matrix'
sensNumber(object) <- value
|
Arguments
cSet |
Parameter name for parent method inherited from CoreGx |
object |
A |
value |
A replacement value |
rSet |
A |
mDataType |
A |
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
annotationA
listof annotation data about the RadioSet, including the$nameand the session information for how the object was creating, detailing the exact versions of R and all the packages usedmolecularProfilesA
listcontaining 4Biobase::ExpressionSettype object for holding data for RNA, DNA, SNP and Copy Number Variation measurements respectively, with associatedfDataandpDatacontaining the row and column metadatacellA
data.framecontaing the annotations for all the cell lines profiled in the data set, across all data typesradiationA
data.framecontaing the annotations for all the radiation treatment types used in the in the dataset, across all data typessensitivityA
listcontaining all the data for the sensitivity experiments, including$info, adata.framecontaining the experimental info,$rawa 3Darraycontaining raw data,$profiles, adata.framecontaining sensitivity profiles statistics, and$n, adata.framedetailing the number of experiments for each cell-radiation type pairperturbationA
listcontainting$n, adata.framesummarizing the available perturbation data,curationA
listcontaining mappings forcellandtissuenames used in the data set to universal identifiers used between different RadioSet objectsdatasetTypeA
characterstring of 'sensitivity', 'perturbation', or both detailing what type of data can be found in the RadioSet, for proper processing of the data
Examples
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 | 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)
|
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