| PharmacoSet-accessors {PharmacoGx} | R Documentation |
PharmacoSetDocumentation for the various setters and getters which allow manipulation
of data in the slots of a PharmacoSet object.
## S4 method for signature 'PharmacoSet' drugInfo(object) ## S4 replacement method for signature 'PharmacoSet,data.frame' drugInfo(object) <- value ## S4 method for signature 'PharmacoSet' drugNames(object) ## S4 replacement method for signature 'PharmacoSet,character' drugNames(object) <- value ## S4 method for signature 'PharmacoSet' annotation(object) ## S4 replacement method for signature 'PharmacoSet,list' annotation(object) <- value ## S4 method for signature 'PharmacoSet' dateCreated(object) ## S4 replacement method for signature 'PharmacoSet,character' dateCreated(object) <- value ## S4 method for signature 'PharmacoSet' name(object) ## S4 replacement method for signature 'PharmacoSet' name(object) <- value ## S4 method for signature 'PharmacoSet' cellInfo(object) ## S4 replacement method for signature 'PharmacoSet,data.frame' cellInfo(object) <- value ## S4 method for signature 'PharmacoSet' cellNames(object) ## S4 replacement method for signature 'PharmacoSet,character' cellNames(object) <- value ## S4 method for signature 'PharmacoSet' curation(object) ## S4 replacement method for signature 'PharmacoSet,list' curation(object) <- value ## S4 method for signature 'PharmacoSet' datasetType(object) ## S4 replacement method for signature 'PharmacoSet,character' datasetType(object) <- 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 method for signature 'PharmacoSet' featureInfo(object, mDataType) ## S4 replacement method for signature 'PharmacoSet,character,data.frame' featureInfo(object, mDataType) <- value ## S4 method for signature 'PharmacoSet,character' phenoInfo(object, mDataType) ## S4 replacement method for signature 'PharmacoSet,character,data.frame' phenoInfo(object, mDataType) <- value ## S4 method for signature 'PharmacoSet,character' fNames(object, mDataType) ## S4 replacement method for signature 'PharmacoSet,character,character' fNames(object, mDataType) <- value ## S4 method for signature 'PharmacoSet' mDataNames(object) ## S4 replacement method for signature 'PharmacoSet' mDataNames(object) <- value ## S4 method for signature 'PharmacoSet' molecularProfilesSlot(object) ## S4 replacement method for signature 'PharmacoSet,list_or_MAE' molecularProfilesSlot(object) <- value ## S4 method for signature 'PharmacoSet' sensitivityInfo(object, dimension, ...) ## S4 replacement method for signature 'PharmacoSet,data.frame' sensitivityInfo(object, dimension, ...) <- value ## S4 method for signature 'PharmacoSet' sensitivityMeasures(object) ## S4 replacement method for signature 'PharmacoSet,character' sensitivityMeasures(object) <- value ## S4 method for signature 'PharmacoSet' sensitivityProfiles(object) ## S4 replacement method for signature 'PharmacoSet,data.frame' sensitivityProfiles(object) <- value ## S4 method for signature 'PharmacoSet' sensitivityRaw(object) ## S4 replacement method for signature 'PharmacoSet,array' sensitivityRaw(object) <- value ## S4 method for signature 'PharmacoSet' sensitivitySlot(object) ## S4 replacement method for signature 'PharmacoSet,list_or_LongTable' sensitivitySlot(object) <- value ## S4 method for signature 'PharmacoSet' sensNumber(object) ## S4 replacement method for signature 'PharmacoSet,matrix' sensNumber(object) <- value ## S4 method for signature 'PharmacoSet' pertNumber(object) ## S4 replacement method for signature 'PharmacoSet,array' pertNumber(object) <- value
object |
A |
value |
See details. |
mDataType |
|
assay |
|
dimension |
See details. |
... |
See details. |
drugInfo: data.frame Retrieve the drug metadata from a
PharmacoSet objects @drug slot.
drugInfo: Update the @drug slot of a PharmacoSet object.
value: data.frame of updated drug metadata to assign to a
PharmacoSet objects @drug slot.
drugNames: character() The names of all drugs available in a specified
PharmacoSet object.
drugNames<-: Set the drug names available in a PharmacoSet object.
value: A character vector of the new drug names. Must have the same
length equal to nrow(drugInfo(object)).
annotation: A list of PharmacoSet 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 PharmacoSet with.
dateCreated: character(1) The date the PharmacoSet object was
created, as returned by the date() function.
dateCreated<-: Update the 'dateCreated' item in the annotation slot of
a PharmacoSet object. Arguments:
value: A character(1) vector, as returned by the date() function.
name: character(1) The name of the PharmacoSet, retreived from
the @annotation slot.
name<-: Update the @annotation$name value in a PharmacoSet object.
value: character(1) The name of the PharmacoSet object.
cellInfo: data.frame Metadata for all cell-lines in a PharmacoSet object.
cellInfo<-: assign updated cell-line annotations to the PharmacoSet object. Arguments:
value: a data.frame object.
cellNames: character Retrieve the rownames of the data.frame in
the cell slot from a PharmacoSet object.
cellNames<-: assign new rownames to the cellInfo slot data.frame for
a PharmacoSet object. Arguments:
value: character vector of rownames for the cellInfo(object) data.frame.
curation: A list of curated mappings between identifiers in the
PharmacoSet object and the original data publication. Contains three data.frames, 'cell' with
cell-line ids and 'tissue' with tissue ids and 'drug' with drug ids.
curation<-: Update the curation slot of a PharmacoSet object. Arugments:
value: A list of data.frames, one for each type of curated
identifier. For a PharmacoSet object the slot should
contain tissue, cell-line and drug id data.frames.
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 PharmacoSet object. Arguments:
value: A character(1) vector with one of 'sensitivity', 'perturbation'
or 'both'
molecularProfiles: matrix() Retrieve an assay in a
SummarizedExperiment from the molecularProfiles slot of a PharmacoSet
object with the specified mDataType. Valid mDataType arguments can be
found with mDataNames(object). Arguments:
assay: Optional character(1) vector specifying an assay in the
SummarizedExperiment of the molecularProfiles slot of the
PharmacoSet 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 PharmacoSet object with the specified
mDataType. Valid mDataType arguments can be found with
mDataNames(object).
assay: Optional character(1) vector specifying an assay in the
SummarizedExperiment of the molecularProfiles slot of the
PharmacoSet 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 PharmacoSet object. More
specifically, retrieve the @rowData slot from the SummarizedExperiment
from the @molecularProfiles of a PharmacoSet 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
PharmacoSet object.
phenoInfo: Return the @colData slot from the SummarizedExperiment of
mDataType, containing sample-level metadata, from a PharmacoSet object.
phenoInfo<-: Update the @colData slot of the SummarizedExperiment
of mDataType in the @molecularProfiles slot of a PharmacoSet 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 PharmacoSet object.
fNames: Updates the rownames of the feature metadata (i.e., rowData)
for a SummarizedExperiment of mDataType within a PharmacoSet object.
value: character() A character vector of new features names for the
rowData of the SummarizedExperiment of mDataType in the
@molecularProfiles slot of a PharmacoSet 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 PharmacoSet 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 PharmacoSet 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 PharmacoSet object. This will either be a list or
MultiAssayExperiment of SummarizedExperiments.
molecularProfilesSlot<-: Update the contents of the @molecularProfiles
slot of a PharmacoSet object. Arguemnts:
value: A list or MultiAssayExperiment of SummarizedExperiments. The
list and assays should be named for the molecular datatype in each
SummarizedExperiment.
dimension: Optional character(1) One of 'drug', 'cell' or 'assay' to
retrieve rowData, colData or the 'assay_metadata' assay from the
PharmacoSet @sensitvity LongTable object, respectively. Ignored with
warning if @sensitivity 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.
sensitivityInfo: DataFrame or data.frame of sensitivity drug combo
by cell-line metadata for the PharmacoSet object. When the dimension
parameter is used, it allows retrieval of the dimension specific metadata
from the LongTable object in @sensitivity of a PharmacoSet object.
sensitivityInfo<-: Update the @sensitivity slot metadata for a
PharmacoSet object. When used without the dimension argument is behaves
similar to the old PharmacoSet 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:
value: A data.frame of treatment response experiment metadata,
documenting experiment level metadata (mapping to drugs and cells). If
the @sensitivity 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 PharmacoSet
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 PharmacoSet
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 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 PharmacoSet
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 PharmacoSet.
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 PharmacoSet
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 PharmacoSet object. Will error when @sensitviity contains
a LongTable object, since the counts are computed on the fly. Arguments:
value: A matrix where rows are cells and columns are drugs, with a
count of the number of experiments for each combination as the values.
pertNumber: array Summary of available perturbation experiments
from in a PharmacoSet 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 PharmacoSet object,
which stores a summary of the available perturbation experiments. Arguments:
value: A new 3D array with the number of perturbation experiments per
drug and cell line, and data type
Accessors: See details.
Setters: An updated PharmacoSet object, returned invisibly.
data(CCLEsmall)
## drug slot
drugInfo(CCLEsmall)
drugInfo(CCLEsmall) <- drugInfo(CCLEsmall)
drugNames(CCLEsmall)
drugNames(CCLEsmall) <- drugNames(CCLEsmall)
## @annotation
annotation(CCLEsmall)
annotation(CCLEsmall) <- annotation(CCLEsmall)
dateCreated(CCLEsmall)
## dateCreated
dateCreated(CCLEsmall) <- date()
name(CCLEsmall)
name(CCLEsmall) <- 'new_name'
cellInfo(CCLEsmall) <- cellInfo(CCLEsmall)
cellNames(CCLEsmall)
cellNames(CCLEsmall) <- cellNames(CCLEsmall)
## curation
curation(CCLEsmall)
curation(CCLEsmall) <- curation(CCLEsmall)
datasetType(CCLEsmall)
datasetType(CCLEsmall) <- 'both'
# No assay specified
molecularProfiles(CCLEsmall, 'rna') <- molecularProfiles(CCLEsmall, 'rna')
# Specific assay
molecularProfiles(CCLEsmall, 'rna', 'exprs') <-
molecularProfiles(CCLEsmall, 'rna', 'exprs')
featureInfo(CCLEsmall, 'rna')
featureInfo(CCLEsmall, 'rna') <- featureInfo(CCLEsmall, 'rna')
phenoInfo(CCLEsmall, 'rna')
phenoInfo(CCLEsmall, 'rna') <- phenoInfo(CCLEsmall, 'rna')
fNames(CCLEsmall, 'rna')
fNames(CCLEsmall, 'rna') <- fNames(CCLEsmall, 'rna')
mDataNames(CCLEsmall)
mDataNames(CCLEsmall) <- mDataNames(CCLEsmall)
molecularProfilesSlot(CCLEsmall)
molecularProfilesSlot(CCLEsmall) <- molecularProfilesSlot(CCLEsmall)
sensitivityInfo(CCLEsmall)
sensitivityInfo(CCLEsmall) <- sensitivityInfo(CCLEsmall)
sensitivityMeasures(CCLEsmall) <- sensitivityMeasures(CCLEsmall)
sensitivityMeasures(CCLEsmall) <- sensitivityMeasures(CCLEsmall)
sensitivityProfiles(CCLEsmall)
sensitivityProfiles(CCLEsmall) <- sensitivityProfiles(CCLEsmall)
head(sensitivityRaw(CCLEsmall))
sensitivityRaw(CCLEsmall) <- sensitivityRaw(CCLEsmall)
sensitivitySlot(CCLEsmall)
sensitivitySlot(CCLEsmall) <- sensitivitySlot(CCLEsmall)
sensNumber(CCLEsmall)
sensNumber(CCLEsmall) <- sensNumber(CCLEsmall)
pertNumber(CCLEsmall)
pertNumber(CCLEsmall) <- pertNumber(CCLEsmall)