Function reference • gDRutils

SE operators

set_SE_fit_parameters() set_SE_processing_metadata() set_SE_keys() set_SE_experiment_metadata() set_SE_experiment_raw_data() get_SE_fit_parameters() get_SE_processing_metadata() get_SE_experiment_raw_data() get_SE_experiment_metadata() get_SE_keys() get_SE_identifiers() set_SE_identifiers(): Get and set metadata for parameters on a SummarizedExperiment object.

aggregate_assay(): Aggregate a BumpyMatrix assay by a given aggregation function.

demote_fields(): Demote a metadata field in the rowData or colData of a SummarizedExperiment object to a nested field of a BumpyMatrix assay.

get_MAE_identifiers(): get_MAE_identifiers

identify_unique_se_metadata_fields(): Identify unique metadata fields from a list of SummarizedExperiments

merge_MAE(): Merge multiple MultiAssayExperiment objects

merge_SE(): Merge multiple Summarized Experiments

merge_assay(): Merge assay data

merge_metadata(): Merge metadata

promote_fields(): Promote a nested field to be represented as a metadata field of the SummarizedExperiment as either the rowData or colData.

split_SE_components(): split_SE_components

Converters

convert_mae_assay_to_dt(): Convert a MultiAssayExperiment assay to a long data.table

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

df_to_bm_assay(): df_to_bm_assay

flatten(): Flatten a table

Identifiers helpers/operators

get_default_identifiers(): Get gDR default identifiers required for downstream analysis.

get_expect_one_identifiers(): Get identifiers that expect only one value for each identifier.

get_identifiers_dt(): Get descriptions for identifiers

get_idfs_synonyms(): Get gDR synonyms for the identifiers

get_required_identifiers(): Get identifiers required for downstream analysis.

get_header(): Get or reset headers for one or all header field(s) respectively

get_env_identifiers() get_prettified_identifiers() set_env_identifier() reset_env_identifiers(): Get, set, or reset identifiers for one or all identifier field(s)

prettify_flat_metrics(): Prettify metric names in flat 'Metrics' assay

update_env_idfs_from_mae(): Update environment identifiers from MAE object identifiers

update_idfs_synonyms(): Update gDR synonyms for the identifier

validate_identifiers(): Check that specified identifier values exist in the data.

Experiment helpers

get_experiment_groups(): get_experiment_groups

get_supported_experiments(): get_supported_experiments

validate_MAE(): Validate MultiAssayExperiment object

validate_SE(): Validate SummarizedExperiment object

validate_dimnames(): Validate dimnames

validate_se_assay_name(): Check whether or not an assay exists in a SummarizedExperiment object.

Assay names

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_combo_assay_names(): get names of combo assays

get_combo_base_assay_names(): get names of combo base assays

get_combo_score_assay_names(): get names of combo score assays

get_env_assay_names(): get default assay names for the specified filters, i.e. set of assay types, assay groups and assay data types

Combination data

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

define_matrix_grid_positions(): Define matrix grid positions

get_additional_variables(): Identify and return additional variables in list of dt

get_combo_excess_field_names(): get names of combo excess fields

get_combo_score_field_names(): get names of combo score fields

has_single_codrug_data(): Has Single Codrug Data

has_valid_codrug_data(): Has Valid Codrug Data

is_combo_data(): Checks if se is combo dataset.

remove_codrug_data(): Remove Codrug Data

round_concentration(): Round concentration to ndigit significant digits

Fit curves

cap_xc50(): Cap XC50 value.

.set_invalid_fit_params(): Set fit parameters for an invalid fit.

fit_curves(): Fit curves

logisticFit(): Logistic fit

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.

predict_smooth_from_combo(): Predict a smoothed response for a drug combination

set_constant_fit_params(): Set fit parameters for a constant fit.

JSON conversion

convert_colData_to_json(): Convert colData to JSON

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_to_json(): Convert a SummarizedExperiment object to a JSON document.

strip_first_and_last_char(): String first and last characters of a string.

validate_mae_with_schema(): Validate MAE against a schema.

JSON validation

validate_json(): Validate JSON against a schema.

JSON const getters

get_isobologram_columns(): Get isobologram column names

get_settings_from_json(): Get settings from JSON file In most common scenario the settings are stored in JSON file to avoid hardcoding

Metadata management

addClass(): add arbitrary S3 class to an object

modifyData(): modify assay with additional data

Standardize MAE

get_optional_coldata_fields(): get optional colData fields

get_optional_rowdata_fields(): get optional rowData fields

refine_coldata(): refine colData

refine_rowdata(): refine rowData

rename_DFrame(): Rename DFrame

rename_bumpy(): Rename BumpyMatrix

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

standardize_mae(): Standardize MAE by switching from custom identifiers into gDR-default

standardize_se(): Standardize SE by switching from custom identifiers into gDR-default

Duplicates

get_assay_dt_duplicated_rows(): Helper function to find duplicated rows in assay data

get_assay_req_uniq_cols(): get columns in the assay data required to have unique data

get_duplicated_rows(): Helper function to find duplicated rows

has_assay_dt_duplicated_rows(): check if assay data contains duplicated data

has_dt_duplicated_rows(): check if data.table contains duplicated data

throw_msg_if_duplicates(): throw message if assay data.table contains duplicated rows

Utils

MAEpply(): Lapply through all the experiments in MultiAssayExperiment object

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.

calc_sd(): Calculate Standard Deviation or Return Zero

cap_assay_infinities(): Cap infinity values (Inf, -Inf) in the assay data

.standardize_conc(): Standardize concentration values.

extend_normalization_type_name(): extend abbreviated normalization type

geometric_mean(): Geometric mean

get_env_var(): safe wrapper of Sys.getenv()

get_gDR_session_info(): get gDR package and their version installed in the environment

get_non_empty_assays(): get_non_empty_assays

get_synthetic_data(): Get synthetic data from gDRtestData package

is_any_exp_empty(): is_any_exp_empty

is_exp_empty(): is_exp_empty

is_mae_empty(): is_mae_empty

loop(): Conditional lapply or bplapply with optional batch processing.

map_conc_to_standardized_conc(): Create a mapping of concentrations to standardized concentrations.

mcolData(): mcolData

mrowData(): mrowData

process_batch(): Process and save a batch of results.

remove_drug_batch(): Remove batch substring from drug id

shorten_normalization_type_name(): shorten normalization type

split_big_table_for_xlsx(): Split big table

Test helpers

gen_synthetic_data(): gen_synthetic_data

get_testdata(): get_testdata

get_testdata_codilution(): get_testdata_codilution

get_testdata_combo(): get_testdata_combo