A package with helper functions for processing drug response
data
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Documentation for package ‘gDRutils’ version 1.5.11
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A C D E F G H I L M P R S T U V misc
-- A --
| addClass | add arbitrary S3 class to an object |
| aggregate_assay | Aggregate a 'BumpyMatrix' assay by a given aggregation function. |
| apply_bumpy_function | Apply a function to every element of a bumpy matrix. |
| assert_choices | assert choices |
| average_biological_replicates_dt | Average biological replicates on the data table side. |
-- C --
| calc_sd | Calculate Standard Deviation or Return Zero |
| cap_assay_infinities | Cap infinity values (Inf, -Inf) in the assay data |
| cap_xc50 | Cap XC50 value. |
| convert_colData_to_json | Convert colData to JSON |
| convert_combo_data_to_dt | convert combo assays from SummarizedExperiments to the list of data.tables |
| convert_combo_field_to_assay | get combo assay names based on the field name |
| convert_mae_assay_to_dt | Convert a MultiAssayExperiment assay to a long data.table |
| convert_mae_to_json | Create JSON document. |
| convert_metadata_to_json | Convert experiment metadata to JSON format for elasticsearch indexing. |
| convert_rowData_to_json | Convert rowData to JSON |
| convert_se_assay_to_custom_dt | Convert a SummarizedExperiment assay to a long data.table and conduct some post processing steps |
| convert_se_assay_to_dt | Convert a SummarizedExperiment assay to a long data.table |
| convert_se_to_json | Convert a SummarizedExperiment object to a JSON document. |
-- D --
| define_matrix_grid_positions | Define matrix grid positions |
| demote_fields | Demote a metadata field in the 'rowData' or 'colData' of a 'SummarizedExperiment' object to a nested field of a 'BumpyMatrix' assay. |
| df_to_bm_assay | df_to_bm_assay |
-- E --
| extend_normalization_type_name | extend abbreviated normalization type |
-- F --
| fit_curves | Fit curves |
| flatten | Flatten a table |
-- G --
| gen_synthetic_data | gen_synthetic_data |
| get_additional_variables | Identify and return additional variables in list of dt |
| get_assay_dt_duplicated_rows | Helper function to find duplicated rows in assay data |
| get_assay_names | 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_req_uniq_cols | get columns in the assay data required to have unique data |
| get_combo_assay_names | get names of combo assays |
| get_combo_base_assay_names | get names of combo base assays |
| get_combo_excess_field_names | get names of combo excess fields |
| get_combo_score_assay_names | get names of combo score assays |
| get_combo_score_field_names | get names of combo score fields |
| get_default_identifiers | Get gDR default identifiers required for downstream analysis. |
| get_duplicated_rows | Helper function to find duplicated rows |
| get_env_assay_names | get default assay names for the specified filters, i.e. set of assay types, assay groups and assay data types |
| get_env_identifiers | Get, set, or reset identifiers for one or all identifier field(s) |
| get_env_var | safe wrapper of Sys.getenv() |
| get_expect_one_identifiers | Get identifiers that expect only one value for each identifier. |
| get_experiment_groups | get_experiment_groups |
| get_header | Get or reset headers for one or all header field(s) respectively |
| get_identifiers_dt | Get descriptions for identifiers |
| get_idfs_synonyms | Get gDR synonyms for the identifiers |
| get_isobologram_columns | Get isobologram column names |
| 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_prettified_identifiers | Get, set, or reset identifiers for one or all identifier field(s) |
| get_required_identifiers | Get identifiers required for downstream analysis. |
| get_settings_from_json | Get settings from JSON file In most common scenario the settings are stored in JSON file to avoid hardcoding |
| get_SE_experiment_metadata | Get and set metadata for parameters on a SummarizedExperiment object. |
| get_SE_experiment_raw_data | Get and set metadata for parameters on a SummarizedExperiment object. |
| get_SE_fit_parameters | Get and set metadata for parameters on a SummarizedExperiment object. |
| get_SE_identifiers | Get and set metadata for parameters on a SummarizedExperiment object. |
| get_SE_keys | Get and set metadata for parameters on a SummarizedExperiment object. |
| get_SE_processing_metadata | Get and set metadata for parameters on a SummarizedExperiment object. |
| get_supported_experiments | get_supported_experiments |
| get_synthetic_data | Get synthetic data from gDRtestData package |
| get_testdata | get_testdata |
| get_testdata_codilution | get_testdata_codilution |
| get_testdata_combo | get_testdata_combo |
-- H --
| has_assay_dt_duplicated_rows | check if assay data contains duplicated data |
| has_dt_duplicated_rows | check if data.table contains duplicated data |
| has_single_codrug_data | Has Single Codrug Data |
| has_valid_codrug_data | Has Valid Codrug Data |
| headers | Get or reset headers for one or all header field(s) respectively |
-- I --
| identifiers | Get, set, or reset identifiers for one or all identifier field(s) |
| identify_unique_se_metadata_fields | Identify unique metadata fields from a list of 'SummarizedExperiment's |
| is_any_exp_empty | is_any_exp_empty |
| is_combo_data | Checks if 'se' is combo dataset. |
| is_exp_empty | is_exp_empty |
| is_mae_empty | is_mae_empty |
-- L --
| logisticFit | Logistic fit |
| loop | Lapply or bplapply. |
-- M --
| MAEpply | Lapply through all the experiments in MultiAssayExperiment object |
| mcolData | mcolData |
| merge_assay | Merge assay data |
| merge_metadata | Merge metadata |
| merge_SE | Merge multiple Summarized Experiments |
| modifyData | modify assay with additional data |
| modifyData.data_source | modify assay with additional data |
| modifyData.default | modify assay with additional data |
| modifyData.drug_name2 | modify assay with additional data |
| mrowData | mrowData |
-- P --
| predict_conc_from_efficacy | Predict a concentration for a given efficacy with fit parameters. |
| predict_efficacy_from_conc | Predict efficacy values given fit parameters and a concentration. |
| prettify_flat_metrics | Prettify metric names in flat 'Metrics' assay |
| promote_fields | Promote a nested field to be represented as a metadata field of the 'SummarizedExperiment' as either the 'rowData' or 'colData'. |
-- R --
| refine_coldata | refine colData |
| refine_rowdata | refine rowData |
| remove_codrug_data | Remove Codrug Data |
| remove_drug_batch | Remove batch substring from drug id |
| rename_bumpy | Rename BumpyMatrix |
| rename_DFrame | Rename DFrame |
| reset_env_identifiers | Get, set, or reset identifiers for one or all identifier field(s) |
| round_concentration | Round concentration to ndigit significant digits |
-- S --
| set_constant_fit_params | Set fit parameters for a constant fit. |
| set_env_identifier | Get, set, or reset identifiers for one or all identifier field(s) |
| set_SE_experiment_metadata | Get and set metadata for parameters on a SummarizedExperiment object. |
| set_SE_experiment_raw_data | Get and set metadata for parameters on a SummarizedExperiment object. |
| set_SE_fit_parameters | Get and set metadata for parameters on a SummarizedExperiment object. |
| set_SE_identifiers | Get and set metadata for parameters on a SummarizedExperiment object. |
| set_SE_keys | Get and set metadata for parameters on a SummarizedExperiment object. |
| set_SE_processing_metadata | Get and set metadata for parameters on a SummarizedExperiment object. |
| set_unique_cl_names | Set Unique Parental Identifiers |
| set_unique_cl_names_dt | Set unique primary cell line identifiers in the table |
| set_unique_drug_names | Set Unique Drug Names |
| set_unique_drug_names_dt | Set unique primary drug identifiers in the table |
| set_unique_identifiers | Set Unique Identifiers in MultiAssayExperiment |
| set_unique_names_dt | Set unique primary identifiers in the data.frame-like objects |
| SE_metadata | Get and set metadata for parameters on a SummarizedExperiment object. |
| shorten_normalization_type_name | shorten normalization type |
| split_SE_components | split_SE_components |
| standardize_mae | Standardize MAE by switching from custom identifiers into gDR-default |
| standardize_se | Standardize SE by switching from custom identifiers into gDR-default |
| strip_first_and_last_char | String first and last characters of a string. |
-- T --
| throw_msg_if_duplicates | throw message if assay data.table contains duplicated rows |
-- U --
| update_env_idfs_from_mae | Update environment identifiers from MAE object identifiers |
| update_idfs_synonyms | Update gDR synonyms for the identifier |
-- V --
| validate_dimnames | Validate dimnames |
| validate_identifiers | Check that specified identifier values exist in the data. |
| validate_json | Validate JSON against a schema. |
| validate_MAE | Validate MultiAssayExperiment object |
| validate_mae_with_schema | Validate MAE against a schema. |
| validate_SE | Validate SummarizedExperiment object |
| validate_se_assay_name | Check whether or not an assay exists in a SummarizedExperiment object. |
-- misc --
| .set_invalid_fit_params | Set fit parameters for an invalid fit. |