Package: gDRutils 1.11.4

Arkadiusz Gladki

gDRutils: A package with helper functions for processing drug response data

This package contains utility functions used throughout the gDR platform to fit data, manipulate data, and convert and validate data structures. This package also has the necessary default constants for gDR platform. Many of the functions are utilized by the gDRcore package.

Authors:Bartosz Czech [aut], Arkadiusz Gladki [cre, aut], Aleksander Chlebowski [aut], Marc Hafner [aut], Pawel Piatkowski [aut], Dariusz Scigocki [aut], Janina Smola [aut], Sergiu Mocanu [aut], Allison Vuong [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gDRutils/json (API)

# Install 'gDRutils' in R:

install.packages('gDRutils', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gdrplatform/gdrutils/issues

Pkgdown/docs site:https://gdrplatform.github.io

On BioConductor:gDRutils-1.11.3(bioc 3.24)gDRutils-1.10.0(bioc 3.23)

software infrastructure

7.74 score 2 stars 3 packages 33 scripts 133 exports 103 dependencies

Last updated from:62009dfc0f. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	207
linux-devel-x86_64	NOTE	405
source / vignettes	OK	287
linux-release-x86_64	NOTE	378
macos-release-arm64	NOTE	251
macos-oldrel-arm64	NOTE	236
windows-devel	NOTE	302
windows-release	NOTE	346
windows-oldrel	NOTE	285
wasm-release	OK	194

Exports:.calculate_complement .clean_key_inputs .set_invalid_fit_params .set_mean_params .setup_metric_output .standardize_conc addClass aggregate_assay apply_bumpy_function assert_choices average_biological_replicates_dt calc_sd cap_assay_infinities cap_xc50 capVals convert_colData_to_json convert_combo_data_to_dt convert_combo_field_to_assay convert_mae_assay_to_dt convert_mae_to_json convert_metadata_to_json convert_rowData_to_json convert_se_assay_to_custom_dt convert_se_assay_to_dt convert_se_to_json define_matrix_grid_positions demote_fields df_to_bm_assay extend_normalization_type_name fit_curves flatten gen_synthetic_data geometric_mean get_additional_variables get_assay_dt_duplicated_rows get_assay_names get_assay_req_uniq_cols get_combo_assay_names get_combo_base_assay_names get_combo_excess_field_names get_combo_score_assay_names get_combo_score_field_names get_default_identifiers get_duplicated_rows get_env_assay_names get_env_identifiers get_env_var get_expect_one_identifiers get_experiment_groups get_gDR_session_info get_header get_identifiers_dt get_idfs_synonyms get_isobologram_columns get_MAE_identifiers get_non_empty_assays get_prettified_identifiers get_required_identifiers get_SE_experiment_metadata get_SE_experiment_raw_data get_SE_fit_parameters get_SE_identifiers get_SE_keys get_SE_processing_metadata get_settings_from_json get_supported_experiments get_synthetic_data get_testdata get_testdata_codilution get_testdata_combo has_assay_dt_duplicated_rows has_dt_duplicated_rows has_single_codrug_data has_valid_codrug_data identify_unique_se_metadata_fields is_any_exp_empty is_combo_data is_exp_empty is_mae_empty logisticFit loop MAEpply map_conc_to_standardized_conc mcolData merge_assay merge_MAE merge_metadata merge_SE modifyData mrowData predict_conc_from_efficacy predict_efficacy_from_conc predict_smooth_from_combo prettify_flat_metrics process_batch promote_fields refine_coldata refine_rowdata remove_codrug_data remove_drug_batch rename_bumpy rename_DFrame reset_env_identifiers round_concentration set_constant_fit_params set_env_identifier set_SE_experiment_metadata set_SE_experiment_raw_data set_SE_fit_parameters set_SE_identifiers set_SE_keys set_SE_processing_metadata set_unique_cl_names set_unique_cl_names_dt set_unique_drug_names set_unique_drug_names_dt set_unique_identifiers set_unique_names_dt shorten_normalization_type_name split_big_table_for_xlsx split_SE_components standardize_mae standardize_se throw_msg_if_duplicates update_drug_name update_env_idfs_from_mae update_idfs_synonyms validate_identifiers validate_json validate_MAE validate_mae_with_schema validate_SE validate_se_assay_name

Dependencies:abind backports Biobase BiocBaseUtils BiocGenerics boot broom BumpyMatrix car carData checkmate cli codetools colorspace cowplot cpp11 curl data.table DelayedArray Deriv digest doBy dplyr drc farver forecast Formula fracdiff generics GenomicRanges ggplot2 glue gtable gtools IRanges isoband jsonlite jsonvalidate labeling lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mgcv microbenchmark minqa modelr multcomp MultiAssayExperiment mvtnorm nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig plotrix purrr qs2 quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel Rdpack reformulas rlang S4Arrays S4Vectors S7 sandwich scales Seqinfo SparseArray SparseM stringfish stringi stringr SummarizedExperiment survival TH.data tibble tidyr tidyselect timeDate urca utf8 V8 vctrs viridisLite withr XVector zoo

gDRutils

Rendered fromgDRutils.Rmdusingknitr::rmarkdown

Last update: 2026-05-28
Started: 2023-03-30

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Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Set fit parameters for an invalid fit.	.set_invalid_fit_params
Standardize concentration values.	.standardize_conc
add arbitrary S3 class to an object	addClass
Aggregate a 'BumpyMatrix' assay by a given aggregation function.	aggregate_assay
Apply a function to every element of a bumpy matrix.	apply_bumpy_function
assert choices	assert_choices
Average biological replicates on the data table side.	average_biological_replicates_dt
Calculate Standard Deviation or Return Zero	calc_sd
Cap infinity values (Inf, -Inf) in the assay data	cap_assay_infinities
Cap XC50 value.	cap_xc50
Convert colData to JSON	convert_colData_to_json
convert combo assays from SummarizedExperiments to the list of data.tables	convert_combo_data_to_dt
get combo assay names based on the field name	convert_combo_field_to_assay
Convert a MultiAssayExperiment assay to a long data.table	convert_mae_assay_to_dt
Create JSON document.	convert_mae_to_json
Convert experiment metadata to JSON format for elasticsearch indexing.	convert_metadata_to_json
Convert rowData to JSON	convert_rowData_to_json
Convert a SummarizedExperiment assay to a long data.table and conduct some post processing steps	convert_se_assay_to_custom_dt
Convert a SummarizedExperiment assay to a long data.table	convert_se_assay_to_dt
Convert a SummarizedExperiment object to a JSON document.	convert_se_to_json
Define matrix grid positions	define_matrix_grid_positions
Demote a metadata field in the 'rowData' or 'colData' of a 'SummarizedExperiment' object to a nested field of a 'BumpyMatrix' assay.	demote_fields
df_to_bm_assay	df_to_bm_assay
extend abbreviated normalization type	extend_normalization_type_name
Fit curves	fit_curves
Flatten a table	flatten
gen_synthetic_data	gen_synthetic_data
Identify and return additional variables in list of dt	get_additional_variables
Helper function to find duplicated rows in assay data	get_assay_dt_duplicated_rows
get assay names of the given se/dataset fetch the data from the se if provided as metadata use predefined values from 'get_env_assay_names' otherwise	get_assay_names
get columns in the assay data required to have unique data	get_assay_req_uniq_cols
get names of combo assays	get_combo_assay_names
get names of combo base assays	get_combo_base_assay_names
get names of combo excess fields	get_combo_excess_field_names
get names of combo score assays	get_combo_score_assay_names
get names of combo score fields	get_combo_score_field_names
Get gDR default identifiers required for downstream analysis.	get_default_identifiers
Helper function to find duplicated rows	get_duplicated_rows
get default assay names for the specified filters, i.e. set of assay types, assay groups and assay data types	get_env_assay_names
safe wrapper of Sys.getenv()	get_env_var
Get identifiers that expect only one value for each identifier.	get_expect_one_identifiers
get_experiment_groups	get_experiment_groups
get gDR package and their version installed in the environment	get_gDR_session_info
Get descriptions for identifiers	get_identifiers_dt
Get gDR synonyms for the identifiers	get_idfs_synonyms
Get isobologram column names	get_isobologram_columns
get_MAE_identifiers	get_MAE_identifiers
get_non_empty_assays	get_non_empty_assays
get optional colData fields	get_optional_coldata_fields
get optional rowData fields	get_optional_rowdata_fields
Get identifiers required for downstream analysis.	get_required_identifiers
Get settings from JSON file In most common scenario the settings are stored in JSON file to avoid hardcoding	get_settings_from_json
get_supported_experiments	get_supported_experiments
Get synthetic data from gDRtestData package	get_synthetic_data
get_testdata	get_testdata
get_testdata_codilution	get_testdata_codilution
get_testdata_combo	get_testdata_combo
check if assay data contains duplicated data	has_assay_dt_duplicated_rows
check if data.table contains duplicated data	has_dt_duplicated_rows
Has Single Codrug Data	has_single_codrug_data
Has Valid Codrug Data	has_valid_codrug_data
Get or reset headers for one or all header field(s) respectively	get_header headers
Get, set, or reset identifiers for one or all identifier field(s)	get_env_identifiers get_prettified_identifiers identifiers reset_env_identifiers set_env_identifier
Identify unique metadata fields from a list of 'SummarizedExperiment's	identify_unique_se_metadata_fields
is_any_exp_empty	is_any_exp_empty
Checks if 'se' is combo dataset.	is_combo_data
is_exp_empty	is_exp_empty
is_mae_empty	is_mae_empty
Logistic fit	logisticFit
Conditional lapply with optional batch processing.	loop
Lapply through all the experiments in MultiAssayExperiment object	MAEpply
Create a mapping of concentrations to standardized concentrations.	map_conc_to_standardized_conc
mcolData	mcolData
Merge assay data	merge_assay
Merge multiple MultiAssayExperiment objects	merge_MAE
Merge metadata	merge_metadata
Merge multiple Summarized Experiments	merge_SE
modify assay with additional data	modifyData modifyData.data_source modifyData.default modifyData.drug_name2
mrowData	mrowData
Predict a concentration for a given efficacy with fit parameters.	predict_conc_from_efficacy
Predict efficacy values given fit parameters and a concentration.	predict_efficacy_from_conc
Predict a smoothed response for a drug combination	predict_smooth_from_combo
Prettify metric names in flat 'Metrics' assay	prettify_flat_metrics
Process and save a batch of results.	process_batch
Promote a nested field to be represented as a metadata field of the 'SummarizedExperiment' as either the 'rowData' or 'colData'.	promote_fields
refine colData	refine_coldata
refine rowData	refine_rowdata
Remove Codrug Data	remove_codrug_data
Remove batch substring from drug id	remove_drug_batch
Rename BumpyMatrix	rename_bumpy
Rename DFrame	rename_DFrame
Round concentration to ndigit significant digits	round_concentration
Get and set metadata for parameters on a SummarizedExperiment object.	get_SE_experiment_metadata get_SE_experiment_raw_data get_SE_fit_parameters get_SE_identifiers get_SE_keys get_SE_processing_metadata set_SE_experiment_metadata set_SE_experiment_raw_data set_SE_fit_parameters set_SE_identifiers set_SE_keys set_SE_processing_metadata SE_metadata
Set fit parameters for a constant fit.	set_constant_fit_params
Set Unique Parental Identifiers	set_unique_cl_names
Set unique primary cell line identifiers in the table	set_unique_cl_names_dt
Set Unique Drug Names	set_unique_drug_names
Set unique primary drug identifiers in the table	set_unique_drug_names_dt
Set Unique Identifiers in MultiAssayExperiment	set_unique_identifiers
Set unique primary identifiers in the data.frame-like objects	set_unique_names_dt
shorten normalization type	shorten_normalization_type_name
Split big table	split_big_table_for_xlsx
split_SE_components	split_SE_components
Standardize MAE by switching from custom identifiers into gDR-default	standardize_mae
Standardize SE by switching from custom identifiers into gDR-default	standardize_se
String first and last characters of a string.	strip_first_and_last_char
throw message if assay data.table contains duplicated rows	throw_msg_if_duplicates
Update environment identifiers from MAE object identifiers	update_env_idfs_from_mae
Update gDR synonyms for the identifier	update_idfs_synonyms
Validate dimnames	validate_dimnames
Check that specified identifier values exist in the data.	validate_identifiers
Validate JSON against a schema.	validate_json
Validate MultiAssayExperiment object	validate_MAE
Validate MAE against a schema.	validate_mae_with_schema
Validate SummarizedExperiment object	validate_SE
Check whether or not an assay exists in a SummarizedExperiment object.	validate_se_assay_name