PharmacoSet-class {PharmacoGx} | R Documentation |
The PharmacoSet (pSet) class was developed to contain and organise large PharmacoGenomic datasets, and aid in their metanalysis. It was designed primarily to allow bioinformaticians and biologists to work with data at the level of genes, drugs 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 drug 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.
Return cell line metadata from a object
Generic for phenoInfo method
Generic for phenoInfo replace method
Generic for molecularProfiles method
Generic for molecularProfiles replace method
Generic for featureInfo method
Generic for featureInfo replace method
Get the senstivity information DataFrame from a object object
Set the sensitivityInfo DataFrame in a object object
Get the sensitivityProfiles data.frame from a object object
Set the sensitivityProfiles in a object object
Get the types of sensitivity measurements from a object object
A generic for the cellNames method
A generic for the cellNames replacement method
Return the feature names for the specified molecular data type
A generic for the dateCreated method
Retrun the name of the PharmacoSet object
A generic for the pertNumber method
A generic for the sensNumber method
A generic for the pertNumber method
A generic for the sensNumber method
## S4 method for signature 'PharmacoSet' cellInfo(object) ## S4 method for signature 'PharmacoSet' drugInfo(object) ## S4 replacement method for signature 'PharmacoSet,data.frame' drugInfo(object) <- value ## S4 method for signature 'PharmacoSet' phenoInfo(object, mDataType) ## S4 replacement method for signature 'PharmacoSet,character,DataFrame' phenoInfo(object, mDataType) <- value ## S4 method for signature 'PharmacoSet' molecularProfiles(object, mDataType, assay) ## S4 replacement method for signature 'PharmacoSet,character,character,matrix' molecularProfiles(object, mDataType, assay) <- value ## S4 replacement method for signature 'PharmacoSet,character,missing,matrix' molecularProfiles(object, mDataType, assay) <- value ## S4 method for signature 'PharmacoSet' featureInfo(object, mDataType) ## S4 replacement method for signature 'PharmacoSet,character,DataFrame' featureInfo(object, mDataType) <- value ## S4 method for signature 'PharmacoSet' sensitivityInfo(object) ## S4 replacement method for signature 'PharmacoSet,data.frame' sensitivityInfo(object) <- value ## S4 method for signature 'PharmacoSet' sensitivityProfiles(object) ## S4 replacement method for signature 'PharmacoSet,data.frame' sensitivityProfiles(object) <- value ## S4 replacement method for signature 'PharmacoSet,matrix' sensitivityProfiles(object) <- value ## S4 method for signature 'PharmacoSet' sensitivityMeasures(object) ## S4 method for signature 'PharmacoSet' drugNames(object) ## S4 replacement method for signature 'PharmacoSet,character' drugNames(object) <- value ## S4 method for signature 'PharmacoSet' cellNames(object) ## S4 replacement method for signature 'PharmacoSet,character' cellNames(object) <- value ## S4 method for signature 'PharmacoSet,character' fNames(object, mDataType) ## S4 method for signature 'PharmacoSet' dateCreated(object) ## S4 method for signature 'PharmacoSet' name(object) ## S4 method for signature 'PharmacoSet' pertNumber(object) ## S4 method for signature 'PharmacoSet' sensNumber(object) ## S4 replacement method for signature 'PharmacoSet,array' pertNumber(object) <- value ## S4 replacement method for signature 'PharmacoSet,matrix' sensNumber(object) <- value
object |
A |
value |
A new |
mDataType |
The molecular data type to return feature names for |
assay |
|
An object of the PharmacoSet class
a data.frame
with the cell annotations
a data.frame
with the experiment info
The updated PharmacoSet
a matrix
of data for the given mDataType and assay
Updated PharmacoSet
a data.frame
with the experiment info
Updated PharmacoSet
a DataFrame
with the experiment info
Updated PharmacoSet
a data.frame
with the experiment info
Updated PharmacoSet
A character
vector of all the available sensitivity measures
A vector of the cell names used in the PharmacoSet
Updated PharmacoSet
A character
vector of the feature names
The date the PharmacoSet was created
The name of the PharmacoSet
A 3D array
with the number of perturbation experiments per
drug and cell line, and data type
A data.frame
with the number of sensitivity experiments per
drug and cell line
The updated PharmacoSet
The updated PharmacoSet
cellInfo
:
drugInfo
: Returns the annotations for all the drugs tested in the PharmacoSet
drugInfo<-
: Update the drug annotations
phenoInfo
: Return the experiment info from the given type of
molecular data in PharmacoSet
phenoInfo<-
: Update the given type of molecular data experiment info in the PharmacoSet
molecularProfiles
: Return the given type of molecular data from the PharmacoSet
molecularProfiles<-
: Update the given type of molecular data from the PharmacoSet
molecularProfiles<-
: Update the given type of molecular data from the PharmacoSet
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 PharmacoSet
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 PharmacoSet was created
name
: Return the name of the PharmacoSet
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
annotation
A list
of annotation data about the PharmacoSet,
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 SummarizedExperiment
type object for holding data for RNA, DNA, SNP and CNV
measurements, with associated fData
and pData
containing the row and column metadata
cell
A data.frame
containing the annotations for all the cell
lines profiled in the data set, across all data types
drug
A data.frame
containg the annotations for all the drugs
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 pair
perturbation
A list
containting $n
, a data.frame
summarizing the available perturbation data,
curation
A list
containing mappings for $drug
,
cell
, tissue
names used in the data set to universal
identifiers used between different PharmacoSet objects
datasetType
A character
string of 'sensitivity',
'perturbation', or both detailing what type of data can be found in the
PharmacoSet, for proper processing of the data
data(CCLEsmall) cellInf <- cellInfo(CCLEsmall) data(CCLEsmall) phenoInf <- phenoInfo(CCLEsmall, mDataType="rna") data(CCLEsmall) phenoInfo(CCLEsmall, mDataType="rna") <- phenoInfo(CCLEsmall, mDataType="rna") data(CCLEsmall) molProf <- molecularProfiles(CCLEsmall, "rna") data(CCLEsmall) molecularProfiles(CCLEsmall, "rna") <- molecularProfiles(CCLEsmall, "rna") data(CCLEsmall) featInf <- featureInfo(CCLEsmall, "rna") data(CCLEsmall) featureInfo(CCLEsmall, "rna") <- featureInfo(CCLEsmall, "rna") data(CCLEsmall) sensInf <- sensitivityInfo(CCLEsmall) data(CCLEsmall) sensitivityInfo(CCLEsmall) <- sensitivityInfo(CCLEsmall) data(CCLEsmall) sensProf <- sensitivityProfiles(CCLEsmall) data(CCLEsmall) sensitivityProfiles(CCLEsmall) <- sensitivityProfiles(CCLEsmall) data(CCLEsmall) sensMeas <- sensitivityMeasures(CCLEsmall) data(CCLEsmall) cellNames(CCLEsmall) data(CCLEsmall) cellNames(CCLEsmall) <- cellNames(CCLEsmall) data(CCLEsmall) fNames(CCLEsmall, "rna") data(CCLEsmall) dateCreated(CCLEsmall) data(CCLEsmall) name(CCLEsmall) data(CCLEsmall) pertNumber(CCLEsmall) data(CCLEsmall) sensNumber(CCLEsmall) data(CCLEsmall) pertNumber(CCLEsmall) <- pertNumber(CCLEsmall) data(CCLEsmall) sensNumber(CCLEsmall) <- sensNumber(CCLEsmall)