.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 |