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