CoreSet-accessors {CoreGx}R Documentation

Accessing and modifying information in a CoreSet

Description

Documentation for the various setters and getters which allow manipulation of data in the slots of a CoreSet object.

Usage

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

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

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

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

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

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

## 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'
treatmentInfo(object)

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

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

## S4 replacement method for signature 'CoreSet,character'
treatmentNames(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,character'
datasetType(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 method for signature 'CoreSet'
featureInfo(object, mDataType)

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

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

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

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

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

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

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

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

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

## S4 method for signature 'CoreSet'
sensitivityInfo(object, dimension, ...)

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

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

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

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

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

Arguments

object

A CoreSet object.

value

See details.

mDataType

character(1) The name of a molecular datatype to access from the molecularProfiles of a CoreSet object.

assay

character(1) A valid assay name in the SummarizedExperiment of @molecularProfiles of a CoreSet object for data type mDataType.

dimension

See details.

...

See details.

Details

@annotation

annotation: A list of CoreSet annotations with items: 'name', the name of the object; 'dateCreated', date the object was created; 'sessionInfo', the sessionInfo() when the object was created; 'call', the R constructor call; and 'version', the object version.

annotation<-: Setter method for the annotation slot. Arguments:

@dateCreated

dateCreated: character(1) The date the CoreSet object was created, as returned by the date() function.

dateCreated<-: Update the 'dateCreated' item in the annotation slot of a CoreSet object. Arguments:

name: character(1) The name of the CoreSet, retreived from the @annotation slot.

name<-: Update the @annotation$name value in a CoreSet object.

cellInfo: data.frame Metadata for all cell-lines in a CoreSet object.

cellInfo<-: assign updated cell-line annotations to the CoreSet object. Arguments:

cellNames: character Retrieve the rownames of the data.frame in the cell slot from a CoreSet object.

cellNames<-: assign new rownames to the cellInfo slot data.frame for a CoreSet object. Arguments:

treatmentInfo: data.frame Metadata for all treatments in a CoreSet object. Arguments:

treatmentInfo<-: CoreSet object with updated treatment metadata. object. Arguments:

treatmentNames: character Names for all treatments in a CoreSet object. Arguments:

treatmentNames<-: CoreSet Object with updates treatment names. object. Arguments:

@curation

curation: A list of curated mappings between identifiers in the CoreSet object and the original data publication. Contains two data.frames, 'cell' with cell-line ids and 'tissue' with tissue ids.

curation<-: Update the curation slot of a CoreSet object. Arugments:

datasetType slot

datasetType: character(1) The type treatment response in the sensitivity slot. Valid values are 'sensitivity', 'perturbation' or 'both'.

datasetType<-: Update the datasetType slot of a CoreSet object. Arguments:

@molecularProfiles

molecularProfiles: matrix() Retrieve an assay in a SummarizedExperiment from the molecularProfiles slot of a CoreSet object with the specified mDataType. Valid mDataType arguments can be found with mDataNames(object). Arguments:

molecularProfiles<-: Update an assay in a SummarizedExperiment from the molecularProfiles slot of a CoreSet object with the specified mDataType. Valid mDataType arguments can be found with mDataNames(object).

featureInfo: Retrieve a DataFrame of feature metadata for the specified mDataType from the molecularProfiles slot of a CoreSet object. More specifically, retrieve the @rowData slot from the SummarizedExperiment from the @molecularProfiles of a CoreSet object with the name mDataType.

featureInfo<-: Update the featureInfo(object, mDataType) DataFrame with new feature metadata. Arguments:

phenoInfo: Return the @colData slot from the SummarizedExperiment of mDataType, containing sample-level metadata, from a CoreSet object.

phenoInfo<-: Update the @colData slot of the SummarizedExperiment of mDataType in the @molecularProfiles slot of a CoreSet object. This updates the sample-level metadata in-place.

fNames: character() The features names from the rowData slot of a SummarizedExperiment of mDataType within a CoreSet object.

fNames: Updates the rownames of the feature metadata (i.e., rowData) for a SummarizedExperiment of mDataType within a CoreSet object.

mDataNames: character Retrieve the names of the molecular data types available in the molecularProfiles slot of a CoreSet object. These are the options which can be used in the mDataType parameter of various molecularProfiles slot accessors methods.

mDataNames: Update the molecular data type names of the molecularProfiles slot of a CoreSet object. Arguments:

molecularProfilesSlot: Return the contents of the @molecularProfiles slot of a CoreSet object. This will either be a list or MultiAssayExperiment of SummarizedExperiments.

molecularProfilesSlot<-: Update the contents of the @molecularProfiles slot of a CoreSet object. Arguemnts:

@sensitivity

Arguments:
Methods:

sensitivityInfo: DataFrame or data.frame of sensitivity drug combo by cell-line metadata for the CoreSet object. When the dimension parameter is used, it allows retrieval of the dimension specific metadata from the LongTable object in @sensitivity of a CoreSet object.

sensitivityInfo<-: Update the @sensitivity slot metadata for a CoreSet object. When used without the dimension argument is behaves similar to the old CoreSet implementation, where the @sensitivity slot contained a list with a $info data.frame item. When the dimension arugment is used, more complicated assignments can occur where 'cell' modifies the @sensitvity LongTable colData, 'drug' the rowData and 'assay' the 'assay_metadata' assay. Arguments:

sensitivityMeaures: Get the 'sensitivityMeasures' available in a CoreSet object. Each measure reprents some summary of cell-line sensitivity to a given dryuh, such as ic50, ec50, AUC, AAC, etc. The results are returned as a character vector with all available metrics for the PSet object.

sensitivityMeaures: Update the sensitivity meaure in a CoreSet object. Thesee values are the column names of the 'profiles' assay and represent various compued sensitviity metrics such as ic50, ec50, AUC, AAC, etc.

sensitivityProfiles: Return the sensitivity profile summaries from the sensitivity slot. This data.frame cotanins vaarious sensitivity summary metrics, such as ic50, amax, EC50, aac, HS, etc as columns, with rows as drug by sample experiments.

sensitivityProfiles<-: Update the sensitivity profile summaries the sensitivity slot. Arguments: -value: A data.frame the the same number of rows as as returned by sensitivityProfiles(object), but potentially modified columns, such as the computation of additional summary metrics.

sensitivityRaw: Access the raw sensitiity measurents for a CoreSet object. A 3D array where rows are experiment_ids, columns are doses and the third dimension is metric, either 'Dose' for the doses used or 'Viability' for the cell-line viability at that dose.

sensitvityRaw<-: Update the raw dose and viability data in a CoreSet.

sensNumber: Return a count of viability observations in a CoreSet object for each drug-combo by cell-line combination.

sensNumber<-: Update the 'n' item, which holds a matrix with a count of drug by cell-line experiment counts, in the list in @sensitivity slot of a CoreSet object. Will error when @sensitviity contains a LongTable object, since the counts are computed on the fly. Arguments:

pertNumber: array Summary of available perturbation experiments from in a CoreSet object. Returns a 3D array with the number of perturbation experiments per drug and cell line, and data type.

pertNumber<-: Update the @perturbation$n value in a CoreSet object, which stores a summary of the available perturbation experiments. Arguments:

Value

Accessors: See details.

Setters: An updated CoreSet object, returned invisibly.

Examples

data(clevelandSmall_cSet)

## @annotation

annotation(clevelandSmall_cSet)

annotation(clevelandSmall_cSet) <- annotation(clevelandSmall_cSet)

dateCreated(clevelandSmall_cSet)

## dateCreated
dateCreated(clevelandSmall_cSet) <- date()

name(clevelandSmall_cSet)

name(clevelandSmall_cSet) <- 'new_name'

cellInfo(clevelandSmall_cSet) <- cellInfo(clevelandSmall_cSet)

cellNames(clevelandSmall_cSet)

cellNames(clevelandSmall_cSet) <- cellNames(clevelandSmall_cSet)

treatmentInfo(clevelandSmall_cSet)

treatmentInfo(clevelandSmall_cSet) <- treatmentInfo(clevelandSmall_cSet)

treatmentNames(clevelandSmall_cSet)

treatmentNames(clevelandSmall_cSet) <- treatmentNames(clevelandSmall_cSet)

## curation
curation(clevelandSmall_cSet)

curation(clevelandSmall_cSet) <- curation(clevelandSmall_cSet)

datasetType(clevelandSmall_cSet)

datasetType(clevelandSmall_cSet) <- 'both'

# No assay specified
molecularProfiles(clevelandSmall_cSet, 'rna') <- molecularProfiles(clevelandSmall_cSet, 'rna')

# Specific assay
molecularProfiles(clevelandSmall_cSet, 'rna', 'exprs') <- 
    molecularProfiles(clevelandSmall_cSet, 'rna', 'exprs')

featureInfo(clevelandSmall_cSet, 'rna')

featureInfo(clevelandSmall_cSet, 'rna') <- featureInfo(clevelandSmall_cSet, 'rna')

phenoInfo(clevelandSmall_cSet, 'rna')

phenoInfo(clevelandSmall_cSet, 'rna') <- phenoInfo(clevelandSmall_cSet, 'rna')

fNames(clevelandSmall_cSet, 'rna')

fNames(clevelandSmall_cSet, 'rna') <- fNames(clevelandSmall_cSet, 'rna')

mDataNames(clevelandSmall_cSet)

mDataNames(clevelandSmall_cSet) <- mDataNames(clevelandSmall_cSet)

molecularProfilesSlot(clevelandSmall_cSet)

molecularProfilesSlot(clevelandSmall_cSet) <- molecularProfilesSlot(clevelandSmall_cSet)

sensitivityInfo(clevelandSmall_cSet)

sensitivityInfo(clevelandSmall_cSet) <- sensitivityInfo(clevelandSmall_cSet)

sensitivityMeasures(clevelandSmall_cSet) <- sensitivityMeasures(clevelandSmall_cSet)

sensitivityMeasures(clevelandSmall_cSet) <- sensitivityMeasures(clevelandSmall_cSet)

sensitivityProfiles(clevelandSmall_cSet)

sensitivityProfiles(clevelandSmall_cSet) <- sensitivityProfiles(clevelandSmall_cSet)

head(sensitivityRaw(clevelandSmall_cSet))

sensitivityRaw(clevelandSmall_cSet) <- sensitivityRaw(clevelandSmall_cSet)

sensitivitySlot(clevelandSmall_cSet)

sensitivitySlot(clevelandSmall_cSet) <- sensitivitySlot(clevelandSmall_cSet)

sensNumber(clevelandSmall_cSet)

sensNumber(clevelandSmall_cSet) <- sensNumber(clevelandSmall_cSet)

pertNumber(clevelandSmall_cSet)

pertNumber(clevelandSmall_cSet) <- pertNumber(clevelandSmall_cSet)


[Package CoreGx version 1.5.7 Index]