CoreSet-accessors: Accessing and modifying information in a 'CoreSet'

In bhklab/CoreGx: Classes and Functions to Serve as the Basis for Other 'Gx' Packages

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'
sampleInfo(object)

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

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

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

## S4 replacement method for signature 'CoreSet,missing,missing,list_OR_MAE'
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'
treatmentResponse(object)

## S4 replacement method for signature 'CoreSet,list_OR_LongTable'
treatmentResponse(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:

• value: a list of annotations to update the CoreSet with.

@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:

• value: A character(1) vector, as returned by the date() function.

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

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

• value: character(1) The name of the CoreSet object.

cellInfo: data.frame Metadata for all sample in a CoreSet object.

sampleInfo<-: assign updated sample annotations to the CoreSet object. Arguments:

• value: a data.frame object.

sampleNames: character Retrieve the rownames of the data.frame in the sample slot from a CoreSet object.

sampleNames<-: assign new rownames to the sampleInfo data.frame for a CoreSet object. Arguments:

• value: character vector of rownames for the sampleInfo(object) data.frame.

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

• object: CoreSet An object to retrieve treatment metadata from.

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

• object: CoreSet An object to set treatment metadata for.

• value: data.frame A new table of treatment metadata for object.

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

• object: CoreSet An object to retrieve treatment names from.

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

• object: CoreSet An object to set treatment names from.

• value: character A character vector of updated treatment names.

@curation

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

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

• value: A list of data.frames, one for each type of curated identifier. For a CoreSet object the slot should contain tissue and sample id data.frames.

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:

• value: A character(1) vector with one of 'sensitivity', 'perturbation' or 'both'

@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). Exclude mDataType and assay to access the entire slot. Arguments:

• assay: Optional character(1) vector specifying an assay in the SummarizedExperiment of the molecularProfiles slot of the CoreSet object for the specified mDataType. If excluded, defaults to modifying the first assay in the SummarizedExperiment for the given mDataType.

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). Omit mDataType and assay to update the slot.

• assay: Optional character(1) vector specifying an assay in the SummarizedExperiment of the molecularProfiles slot of the CoreSet object for the specified mDataType. If excluded, defaults to modifying the first assay in the SummarizedExperiment for the given mDataType.

• value: A matrix of values to assign to the assay slot of the SummarizedExperiment for the selected mDataType. The rownames and column names must match the associated SummarizedExperiment.

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:

• value: A data.frame or DataFrame with updated feature metadata for the specified molecular profile in the molecularProfiles slot of a CoreSet object.

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.

• value: A data.frame or DataFrame object where rows are samples and columns are sample metadata.

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.

• value: character() A character vector of new features names for the rowData of the SummarizedExperiment of mDataType in the ⁠@molecularProfiles⁠ slot of a CoreSet object. Must be the same length as nrow(featureInfo(object, mDataType)), the number of rows in the feature metadata.

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:

• value: character vector of molecular datatype names, with length equal to length(molecularProfilesSlot(object)).

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:

• value: A list or MultiAssayExperiment of SummarizedExperiments. The list and assays should be named for the molecular datatype in each SummarizedExperiment.

@treatmentResponse

Arguments:

• dimension: Optional character(1) One of 'treatment', 'sample' or 'assay' to retrieve rowData, colData or the 'assay_metadata' assay from the CoreSet ⁠@sensitvity⁠ LongTable object, respectively. Ignored with warning if ⁠@treatmentResponse⁠ is not a LongTable object.

• ...: Additional arguments to the rowData or colData. LongTable methods. Only used if the sensitivity slot contains a LongTable object instead of a list and the dimension argument is specified.

Methods:

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

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

• value: A data.frame of treatment response experiment metadata, documenting experiment level metadata (mapping to treatments and samples). If the ⁠@treatmentResponse⁠ slot doesn't contain a LongTable and dimension is not specified, you can only modify existing columns as returned by sensitivityInfo(object).

sensitivityMeaures: Get the 'sensitivityMeasures' available in a CoreSet object. Each measure reprents some summary of sample sensitivity to a given treatment, 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.

• value: A character vector of new sensitivity measure names, the then length of the character vector must matcht he number of columns of the 'profiles' assay, excluding metadata and key columns.

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 treatment 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 sample viability at that dose.

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

• value: A 3D array object where rows are experiment_ids, columns are replicates and pages are c('Dose', 'Viability'), with the corresponding dose or viability measurement for that experiment_id and replicate.

sensNumber: Return a count of viability observations in a CoreSet object for each treatment-combo by sample combination.

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

• value: A matrix where rows are samples and columns are treatments, with a count of the number of experiments for each combination as the values.

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

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

• value: A new 3D array with the number of perturbation experiments per treatment and sample, and data type

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'

sampleInfo(clevelandSmall_cSet) <- sampleInfo(clevelandSmall_cSet)

sampleNames(clevelandSmall_cSet)

sampleNames(clevelandSmall_cSet) <- sampleNames(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')

# Replace the whole slot
molecularProfiles(clevelandSmall_cSet) <- molecularProfiles(clevelandSmall_cSet)

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)

treatmentResponse(clevelandSmall_cSet)

treatmentResponse(clevelandSmall_cSet) <- treatmentResponse(clevelandSmall_cSet)

sensNumber(clevelandSmall_cSet)

sensNumber(clevelandSmall_cSet) <- sensNumber(clevelandSmall_cSet)

pertNumber(clevelandSmall_cSet)

pertNumber(clevelandSmall_cSet) <- pertNumber(clevelandSmall_cSet)

bhklab/CoreGx documentation built on March 14, 2024, 3:04 a.m.