Package index
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AssayTypes - An enumeration of supported assay types
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DrugResponseAssay-class - DrugResponseAssay S4 class definition
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DrugResponseAssay() - Create a DrugResponseAssay object
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ExpressionAssay-class - ExpressionAssay S4 class definition
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ExpressionAssay() - Create an ExpressionAssay object
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ModelMetadataFields - ModelMetadataFields
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OncoExperiment-class - OncoExperiment S4 class definition
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OncoExperiment() - Create an empty OncoExperiment object
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ProteinExpressionAssay-class - ProteinExpressionAssay S4 class definition
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RNAAssay() - Create a ProteinExpressionAssay object
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SensitivityUnits - Drug sensitivity response units LFC = log fold change, AUC = area under the curve, IC50 = half maximal inhibitory concentration
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add_assay(<OncoExperiment>,<SummarizedExperiment>) - Add an assay experiment to an OncoExperiment
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add_assay() - Add an assay to an object
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compare_drug_sensitivities(<OncoExperiment>) - Compare drug sensitivities between two OncoExperiment groups
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compare_drug_sensitivities() - Compare drug sensitivities between two groups
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export(<DrugSensitivityComparison>) - Export a `DrugSensitivityComparison` object
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load_assays(<OncoExperiment>) - Load assay data into an OncoExperiment object
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load_assays() - Load assay data into an OncoExperiment object The function will coerce the assay into the corresponding OncoAssay class before being added to the OncoExperiment object.
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plot_donut(<OncoExperiment>) - Create a donut plot from model metadata
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plot_donut() - Create a donut plot
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show(<OncoExperiment>) - Show an OncoExperiment object
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subset(<OncoExperiment>) - Subset an OncoExperiment
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subset() - Subset an OncoExperiment