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

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Documentation for package ‘gDRcore’ version 1.3.13

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

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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	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_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_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