CoreSet-class {CoreGx} | R Documentation |
CoreSet - A generic data container for molecular profiles and treatment response data
The CoreSet (CSet) class was developed as a superclass for pSets in the PharmacoGx and RadioGx packages to contain the data generated in screens of cancer cell lines for their genetic profile and sensitivities to therapy (Pharmacological or Radiation). This class is meant to be a superclass which is contained within the PharmacoSet (pSet) and RadioSet (RSet) objects exported by PharmacoGx and RadioGx. The format of the data is similar for both pSets and rSets, allowing much of the code to be abstracted into the CoreSet super-class. However, the models involved with quantifying cellular response to Pharmacological and Radiation therapy are widely different, and extension of the cSet class allows the packages to apply the correct model for the given data.
annotation
See Slots section.
molecularProfiles
See Slots section.
cell
See Slots section.
curation
See Slots section.
sensitivity
See Slots section.
perturbation
See Slots section.
curation
See Slots section.
datasetType
See Slots section.
annotation: A list
of annotation data about the CoreSet
,
including the $name
and the session information for how the object
was created, detailing the exact versions of R and all the packages used.
molecularProfiles: A list
or MultiAssayExperiment
containing
CoreSet
object.
cell: A data.frame
containg the annotations for all the cell
lines profiled in the data set, across all molecular data types and
treatment response experiments.
sensitivity: A list
or LongTable
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/radiationInfo pair
perturbation: list
containing $n
, a data.frame
summarizing the available perturbation data. This slot is currently
being deprecated.
curation: list
containing mappings for
cell
, tissue
names used in the data set to universal
identifiers used between different CoreSet
objects
datasetType: character
string of 'sensitivity',
'perturbation', or both detailing what type of data can be found in the
CoreSet, for proper processing of the data