# Processing functions and interface to process and analyze drug dose-response data

## Documentation for package ‘gDRcore’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.calculate_matrix_metric | Calculate a metric for combination data.
.map_references | Map references
.standardize_conc | Standardize concentration values.
annotate_dt_with_cell_line | annotate_dt_with_cell_line
annotate_dt_with_drug | annotate_dt_with_drug
average_SE | Run drug response processing pipeline
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_score | Calculate score for HSA and Bliss
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 | Run drug response processing pipeline
create_SE | Run drug response processing pipeline
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
fit_SE | Run drug response processing pipeline
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_cellline_annotation_from_dt | Retrieve the cell line annotation from the annotated dt input
get_cell_line_annotation | get_cell_line_annotation
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
get_drug_annotation | get_drug_annotation
get_drug_annotation_from_dt | Retrieve the drug annotation from the annotated dt input
grr_matches | Value Matching
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.
map_untreated | Identify untreated rows based on Drug treatment alone
merge_data | merge_data
normalize_SE | Run drug response processing pipeline
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
process_perturbations | Cleanup additional perturbations in the data.table
remove_drug_batch | Remove batch from Gnumber
replace_conc_with_standardized_conc | Standardize concentrations.
runDrugResponseProcessingPipeline | Run drug response processing pipeline
runDrugResponseProcessingPipelineFxns | Run drug response processing pipeline
split_raw_data | Split raw data into list based on the data types
test_synthetic_data | Testing synthetic data form gDRtestData package