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

# A package with helper functions for processing drug response data

## Documentation for package ‘gDRutils’ version 1.9.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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_gDR_session_info | get gDR package and their version installed in the environment
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 | Conditional lapply or bplapply with optional batch processing.

## -- M --

MAEpply | Lapply through all the experiments in MultiAssayExperiment object
map_conc_to_standardized_conc | Create a mapping of concentrations to standardized concentrations.
mcolData | mcolData
merge_assay | Merge assay data
merge_MAE | Merge multiple MultiAssayExperiment objects
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.
predict_smooth_from_combo | Predict a smoothed response for a drug combination
prettify_flat_metrics | Prettify metric names in flat 'Metrics' assay
process_batch | Process and save a batch of results.
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_big_table_for_xlsx | Split big table
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.
.standardize_conc | Standardize concentration values.