Package: gDRutils 1.5.5

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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gDRutils.pdf |gDRutils.html✨
gDRutils/json (API)
NEWS

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

Peer review:

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

Pkgdown:https://gdrplatform.github.io

On BioConductor:gDRutils-1.5.4(bioc 3.21)gDRutils-1.4.0(bioc 3.20)

softwareinfrastructure

7.10 score 3 packages 3 scripts 146 downloads 123 exports 107 dependencies

Last updated 6 days agofrom:10a0dcc3ed. Checks:OK: 3 NOTE: 2 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winNOTEDec 18 2024
R-4.5-linuxNOTEDec 18 2024
R-4.4-winOKDec 18 2024
R-4.4-macOKDec 18 2024
R-4.3-winERRORDec 18 2024
R-4.3-macERRORDec 18 2024

Exports:.calculate_complement.clean_key_inputs.set_invalid_fit_params.set_mean_params.setup_metric_outputaddClassaggregate_assayapply_bumpy_functionassert_choicesaverage_biological_replicates_dtcalc_sdcap_xc50capValsconvert_colData_to_jsonconvert_combo_data_to_dtconvert_combo_field_to_assayconvert_mae_assay_to_dtconvert_mae_to_jsonconvert_metadata_to_jsonconvert_rowData_to_jsonconvert_se_assay_to_custom_dtconvert_se_assay_to_dtconvert_se_to_jsondefine_matrix_grid_positionsdemote_fieldsdf_to_bm_assayextend_normalization_type_namefit_curvesflattengen_synthetic_datageometric_meanget_additional_variablesget_assay_dt_duplicated_rowsget_assay_namesget_assay_req_uniq_colsget_combo_assay_namesget_combo_base_assay_namesget_combo_excess_field_namesget_combo_score_assay_namesget_combo_score_field_namesget_default_identifiersget_duplicated_rowsget_env_assay_namesget_env_identifiersget_env_varget_expect_one_identifiersget_experiment_groupsget_headerget_identifiers_dtget_idfs_synonymsget_isobologram_columnsget_MAE_identifiersget_non_empty_assaysget_prettified_identifiersget_required_identifiersget_SE_experiment_metadataget_SE_experiment_raw_dataget_SE_fit_parametersget_SE_identifiersget_SE_keysget_SE_processing_metadataget_settings_from_jsonget_supported_experimentsget_synthetic_dataget_testdataget_testdata_codilutionget_testdata_combohas_assay_dt_duplicated_rowshas_dt_duplicated_rowshas_single_codrug_datahas_valid_codrug_dataidentify_unique_se_metadata_fieldsis_any_exp_emptyis_combo_datais_exp_emptyis_mae_emptylogisticFitloopMAEpplymcolDatamerge_assaymerge_metadatamerge_SEmodifyDatamrowDatapredict_conc_from_efficacypredict_efficacy_from_concprettify_flat_metricspromote_fieldsrefine_coldatarefine_rowdataremove_codrug_datarename_bumpyrename_DFramereset_env_identifiersround_concentrationset_constant_fit_paramsset_env_identifierset_SE_experiment_metadataset_SE_experiment_raw_dataset_SE_fit_parametersset_SE_identifiersset_SE_keysset_SE_processing_metadataset_unique_cl_namesset_unique_cl_names_dtset_unique_drug_namesset_unique_drug_names_dtset_unique_identifiersset_unique_names_dtshorten_normalization_type_namesplit_SE_componentsstandardize_maestandardize_sethrow_msg_if_duplicatesupdate_env_idfs_from_maeupdate_idfs_synonymsvalidate_identifiersvalidate_jsonvalidate_MAEvalidate_mae_with_schemavalidate_SEvalidate_se_assay_name

Dependencies:abindaskpassbackportsBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbootbroomBumpyMatrixcarcarDatacheckmateclicodetoolscolorspacecowplotcpp11crayoncurldata.tableDelayedArrayDerivdoBydplyrdrcfansifarverformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablegtoolshttrIRangesisobandjsonlitejsonvalidatelabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmultcompMultiAssayExperimentmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplotrixpurrrquantregR6RColorBrewerRcppRcppEigenrlangS4ArraysS4VectorssandwichscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsysTH.datatibbletidyrtidyselectUCSC.utilsutf8V8vctrsviridisLitewithrXVectorzlibbioczoo

gDRutils

gDR team

Rendered fromgDRutils.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-07-04
Started: 2023-03-30

Readme and manuals

Help Manual

Help pageTopics
Set fit parameters for an invalid fit..set_invalid_fit_params
add arbitrary S3 class to an objectaddClass
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 choicesassert_choices
Average biological replicates on the data table side.average_biological_replicates_dt
Calculate Standard Deviation or Return Zerocalc_sd
Cap XC50 value.cap_xc50
Convert colData to JSONconvert_colData_to_json
convert combo assays from SummarizedExperiments to the list of data.tablesconvert_combo_data_to_dt
get combo assay names based on the field nameconvert_combo_field_to_assay
Convert a MultiAssayExperiment assay to a long data.tableconvert_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 JSONconvert_rowData_to_json
Convert a SummarizedExperiment assay to a long data.table and conduct some post processing stepsconvert_se_assay_to_custom_dt
Convert a SummarizedExperiment assay to a long data.tableconvert_se_assay_to_dt
Convert a SummarizedExperiment object to a JSON document.convert_se_to_json
Define matrix grid positionsdefine_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_assaydf_to_bm_assay
extend abbreviated normalization typeextend_normalization_type_name
Fit curvesfit_curves
Flatten a tableflatten
gen_synthetic_datagen_synthetic_data
Identify and return additional variables in list of dtget_additional_variables
Helper function to find duplicated rows in assay dataget_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' otherwiseget_assay_names
get columns in the assay data required to have unique dataget_assay_req_uniq_cols
get names of combo assaysget_combo_assay_names
get names of combo base assaysget_combo_base_assay_names
get names of combo excess fieldsget_combo_excess_field_names
get names of combo score assaysget_combo_score_assay_names
get names of combo score fieldsget_combo_score_field_names
Get gDR default identifiers required for downstream analysis.get_default_identifiers
Helper function to find duplicated rowsget_duplicated_rows
get default assay names for the specified filters, i.e. set of assay types, assay groups and assay data typesget_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_groupsget_experiment_groups
Get descriptions for identifiersget_identifiers_dt
Get gDR synonyms for the identifiersget_idfs_synonyms
Get isobologram column namesget_isobologram_columns
get_MAE_identifiersget_MAE_identifiers
get_non_empty_assaysget_non_empty_assays
get optional colData fieldsget_optional_coldata_fields
get optional rowData fieldsget_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 hardcodingget_settings_from_json
get_supported_experimentsget_supported_experiments
Get synthetic data from gDRtestData packageget_synthetic_data
get_testdataget_testdata
get_testdata_codilutionget_testdata_codilution
get_testdata_comboget_testdata_combo
check if assay data contains duplicated datahas_assay_dt_duplicated_rows
check if data.table contains duplicated datahas_dt_duplicated_rows
Has Single Codrug Datahas_single_codrug_data
Has Valid Codrug Datahas_valid_codrug_data
Get or reset headers for one or all header field(s) respectivelyget_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'sidentify_unique_se_metadata_fields
is_any_exp_emptyis_any_exp_empty
Checks if 'se' is combo dataset.is_combo_data
is_exp_emptyis_exp_empty
is_mae_emptyis_mae_empty
Logistic fitlogisticFit
Lapply or bplapply.loop
Lapply through all the experiments in MultiAssayExperiment objectMAEpply
mcolDatamcolData
Merge assay datamerge_assay
Merge metadatamerge_metadata
Merge multiple Summarized Experimentsmerge_SE
modify assay with additional datamodifyData modifyData.data_source modifyData.default modifyData.drug_name2
mrowDatamrowData
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
Prettify metric names in flat 'Metrics' assayprettify_flat_metrics
Promote a nested field to be represented as a metadata field of the 'SummarizedExperiment' as either the 'rowData' or 'colData'.promote_fields
refine colDatarefine_coldata
refine rowDatarefine_rowdata
Remove Codrug Dataremove_codrug_data
Rename BumpyMatrixrename_bumpy
Rename DFramerename_DFrame
Round concentration to ndigit significant digitsround_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 Identifiersset_unique_cl_names
Set unique primary cell line identifiers in the tableset_unique_cl_names_dt
Set Unique Drug Namesset_unique_drug_names
Set unique primary drug identifiers in the tableset_unique_drug_names_dt
Set Unique Identifiers in MultiAssayExperimentset_unique_identifiers
Set unique primary identifiers in the data.frame-like objectsset_unique_names_dt
shorten normalization typeshorten_normalization_type_name
split_SE_componentssplit_SE_components
Standardize MAE by switching from custom identifiers into gDR-defaultstandardize_mae
Standardize SE by switching from custom identifiers into gDR-defaultstandardize_se
String first and last characters of a string.strip_first_and_last_char
throw message if assay data.table contains duplicated rowsthrow_msg_if_duplicates
Update environment identifiers from MAE object identifiersupdate_env_idfs_from_mae
Update gDR synonyms for the identifierupdate_idfs_synonyms
Validate dimnamesvalidate_dimnames
Check that specified identifier values exist in the data.validate_identifiers
Validate JSON against a schema.validate_json
Validate MultiAssayExperiment objectvalidate_MAE
Validate MAE against a schema.validate_mae_with_schema
Validate SummarizedExperiment objectvalidate_SE
Check whether or not an assay exists in a SummarizedExperiment object.validate_se_assay_name