PharmacoSet-accessors {PharmacoGx} | R Documentation |
PharmacoSet
Documentation 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.frame
s, '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.frame
s, one for each type of curated
identifier. For a PharmacoSet
object the slot should
contain tissue, cell-line and drug id data.frame
s.
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 SummarizedExperiment
s.
molecularProfilesSlot<-: Update the contents of the @molecularProfiles
slot of a PharmacoSet
object. Arguemnts:
value: A list
or MultiAssayExperiment
of SummarizedExperiment
s. 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)