Processing functions and interface to process and analyze drug
dose-response data
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Documentation for package ‘gDRcore’ version 1.0.1
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| .calculate_matrix_metric | Calculate a metric for combination data. |
| .map_references | Map references |
| .standardize_conc | Standardize concentration values. |
| add_CellLine_annotation | add_CellLine_annotation |
| add_Drug_annotation | add_Drug_annotation |
| average_SE | If a column called '"BackgroundValue"' exists in 'df_', it will be removed from the 'readout' column. |
| calculate_Bliss | Calculate a metric for combination data. |
| calculate_endpt_GR_value | Calculate a GR value. |
| calculate_excess | Calculate the difference between values in two data.tables |
| calculate_GR_value | Calculate a GR value. |
| calculate_HSA | Calculate a metric for combination data. |
| calculate_matrix_metric | Calculate a metric for combination data. |
| calculate_time_dep_GR_value | Calculate a GR value. |
| cleanup_metadata | cleanup_metadata |
| convert_mae_to_raw_data | Transform mae into raw data |
| convert_se_to_raw_data | Transform se into raw_data |
| create_and_normalize_SE | If a column called '"BackgroundValue"' exists in 'df_', it will be removed from the 'readout' column. |
| create_SE | If a column called '"BackgroundValue"' exists in 'df_', it will be removed from the 'readout' column. |
| data_model | Detect model of data |
| data_model.character | Detect model of data from experiment name |
| data_model.data.table | Detect model of data in data.table |
| define_matrix_grid_positions | Define matrix grid positions |
| fit_SE | If a column called '"BackgroundValue"' exists in 'df_', it will be removed from the 'readout' column. |
| fit_SE.combinations | fit_SE for combination screens |
| get_assays_per_pipeline_step | get info about created/present assays in SE at the given pipeline step |
| get_default_nested_identifiers | Get default nested identifiers |
| get_default_nested_identifiers.data.table | Get default nested identifiers |
| get_default_nested_identifiers.SummarizedExperiment | Get default nested identifiers |
| identify_data_type | Identify type of data |
| identify_keys | identify_keys |
| map_conc_to_standardized_conc | Create a mapping of concentrations to standardized concentrations. |
| map_df | Map treated conditions to their respective references. |
| map_ids_to_fits | Get predicted values for a given fit and input. |
| matches | Value Matching |
| merge_data | merge_data |
| normalize_SE | If a column called '"BackgroundValue"' exists in 'df_', it will be removed from the 'readout' column. |
| order_result_df | Order_result_df |
| prepare_input | Prepare input data common for all experiments |
| prepare_input.data.table | Prepare input data common for all experiments |
| prepare_input.MultiAssayExperiment | Prepare input data common for all experiments |
| remove_drug_batch | Remove batch from Gnumber |
| replace_conc_with_standardized_conc | Standardize concentrations. |
| round_concentration | Round concentration to ndigit significant digits |
| runDrugResponseProcessingPipeline | If a column called '"BackgroundValue"' exists in 'df_', it will be removed from the 'readout' column. |
| runDrugResponseProcessingPipelineFxns | If a column called '"BackgroundValue"' exists in 'df_', it will be removed from the 'readout' column. |
| split_raw_data | Split raw data into list based on the data types |
| test_synthetic_data | Testing synthetic data form gDRtestData package |