Package index • gDRcore

Pipeline

Run different components of the gDR drug response processing pipeline. Either create a SummarizedExperiment and normalize raw treated and control data (create_and_normalize_SE), average data (average_SE), or fit the processed data (fit_SE).

compute_growth_rates(): Compute per-period growth rates for time-course screens
fit_SE.combinations(): fit_SE for combination screens
fit_SE.timecourse(): fit_SE for time-course (Incucyte) screens
get_period_timepoints(): List the measurement timepoints entering each growth-rate window
growth_rates_to_se(): Convert a growth rate table into the stage 2 SummarizedExperiment
average_SE() create_SE() fit_SE() normalize_SE() create_and_normalize_SE() runDrugResponseProcessingPipeline(): Run drug response processing pipeline

Merging data

merge_data(): merge_data

Combination helpers

calculate_excess(): Calculate the difference between values in two data.tables
calculate_HSA() calculate_Bliss() .calculate_matrix_metric(): Calculate a metric for combination data.
calculate_score(): Calculate score for HSA and Bliss

Annotation

annotate_dt_with_cell_line(): annotate_dt_with_cell_line
annotate_dt_with_drug(): annotate_dt_with_drug
annotate_mae_with_cell_line(): annotate_mae_with_cell_line
annotate_mae_with_drug(): annotate_mae_with_drug
annotate_se_with_cell_line(): annotate_se_with_cell_line
annotate_se_with_drug(): annotate_se_with_drug
get_cell_line_annotation(): get_cell_line_annotation
get_cellline_annotation_from_dt(): Retrieve the cell line annotation from the annotated dt input
get_drug_annotation(): get_drug_annotation
get_drug_annotation_from_dt(): Retrieve the drug annotation from the annotated dt input

Calculating GR

calculate_GR_value() calculate_time_dep_GR_value() calculate_endpt_GR_value(): Calculate a GR value.

Converting to raw data

convert_mae_to_raw_data(): Transform mae into raw data
convert_se_to_raw_data(): Transform se into raw_data

Data type

identify_data_type(): Identify type of data
process_perturbations(): Cleanup additional perturbations in the data.table
split_raw_data(): Split raw data into list based on the data types

Preparing input

prepare_input(<MultiAssayExperiment>): Prepare input data common for all experiments
prepare_input(): Prepare input data common for all experiments
prepare_input(<data.table>): Prepare input data common for all experiments

Mappping

.map_references(): Map references
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

Utils

cleanup_metadata(): cleanup_metadata
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
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
grr_matches(): Value Matching
identify_keys(): identify_keys
order_result_df(): Order_result_df
replace_conc_with_standardized_conc(): Standardize concentrations.

Test utils

test_synthetic_data(): Testing synthetic data form gDRtestData package

Combination fit interface

Reference implementations for combination synergy scoring, applied through the generic fit interface in gDRutils.

apply_combo_sa_fits(): apply_combo_sa_fits
apply_combo_excess(): apply_combo_excess
apply_combo_isobolograms(): apply_combo_isobolograms
apply_combo_scores(): apply_combo_scores
bliss_fit_fn(): bliss_fit_fn
hss_fit_fn(): hss_fit_fn

Moved to gDRutils

The generic fit interface and the fit profile registry now live in gDRutils. They are re-exported here for one release cycle, together with the two deprecated aliases.

reexports apply_fit apply_fit_to_se apply_fits fit_drug_response_metrics fit_drug_response_metrics_4p get_fit_profile get_fit_profiles register_fit_profile: Objects exported from other packages
apply_custom_fit(): Deprecated alias for apply_fit
apply_custom_fits(): Deprecated alias for apply_fits