A package with helper functions for processing drug response data

Documentation for package ‘gDRutils’ version 1.3.5

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-- A --

addClass	add arbitrary S3 class to an object
aggregate_assay	Aggregate a 'BumpyMatrix' assay by a given aggreation 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.

-- C --

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_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_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_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_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
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.
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.

-- 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.