Function reference • gDRimport

Load files

enhance_raw_edited_EnVision_df(): Enhance raw edited EnVision data.table

get_EnVision_properties(): Get properties of EnVision data

get_df_from_raw_edited_EnVision_df(): Get final results (as a data.table) from raw edited EnVision data.table

get_df_from_raw_unedited_EnVision_df(): Get final results (as a data.table) from raw unedited EnVision data.table

get_excel_sheet_names(): get Excel sheets names for a charvec of files for non-Excel files return 0

get_plate_info_from_template_xlsx(): Get plate info from template xlsx

load_data(): Load data

load_manifest(): Load manifest

load_results(): Load results

load_results_EnVision(): Load EnVision results from xlsx

load_results_Tecan(): Load tecan results from xlsx

load_results_tsv(): Load results from tsv

load_templates(): Load templates

load_templates_tsv(): Load templates from tsv

load_templates_xlsx(): Load templates from xlsx

read_EnVision_delim(): Read EnVision delimited text files

read_EnVision_xlsx(): Read in single xlsx data from EnVision

read_in_EnVision_file(): Read EnVision file

read_in_manifest_file(): read manifest files

read_in_result_files(): Read in results files

read_in_results_Tecan(): read in Tecan data

read_in_template_sheet_xlsx(): Read in data from xlsx template sheet

read_in_template_xlsx(): Read in xlsx template files

read_in_tsv_template_files(): read in tsv template files

validate_template_xlsx(): Validate template xlsx data

Pset conversion

convert_MAE_to_PSet(): Convert MultiAssayExperiment to TreatmentResponseExperiment

convert_pset_to_df(): Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline

.extract_or_create_assay(): Extracts an assay from a SummarizedExperiment object or creates a new one if it does not exist

getPSet(): Get PharmacoSet

setEnvForPSet(): Adjust environment variables to meet gDR standards

Import D300

import_D300(): Import D300

parse_D300_xml(): Parse D300

save_drug_info_per_well(): for each drug create a Gnumber and Concentration information for each well

Input data validation/correction

are_template_sheets_valid(): are template sheet valid?

check_metadata_against_spaces(): Check metadata against spaces

check_metadata_field_names(): Check metadata field names

check_metadata_headers(): Check whether metadata headers are correct and make fixes if needed

check_metadata_names(): check_metadata_names

check_metadata_req_col_names(): Check metadata for required column names

correct_template_sheets(): Correct names of the template sheets (if required)

.check_against_single_template_sheet(): Evaluate if template file with single sheet is present, if the name of the sheet is correct and if it can be fixed

fix_typos_with_reference(): Fix typos using reference data

get_exception_data(): get exception data

get_expected_template_sheets(): Get names of the sheets expected in templates xlsx

get_xl_sheets(): Get Excel sheets

mgrepl(): grep wrapper to support multiple patterns

Utils

detect_file_format(): Detect format of results data

is_readable_v(): is_readable_v Check if all paths in vector are readable

read_excel_to_dt(): Read excel file and transorm it into data.table object

read_ref_data(): read_ref_data

standardize_record_values(): standardize_record_values

Test data class

gdr_test_data-class: gDR Test Data object

get_test_data(): get primary test data

manifest_path(): Method manifest_path

result_path(): Method result_path

template_path(): Method template_path

Test data

get_test_D300_data(): get test D300 data

get_test_EnVision_data(): get test EnVision data

get_test_Tecan_data(): get test Tecan data

get_test_tsv_data(): get test tsv data