Package for handling the import of dose-response data

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Documentation for package ‘gDRimport’ version 1.3.2

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

Help Pages

.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
.extract_or_create_assay	Extracts an assay from a SummarizedExperiment object or creates a new one if it does not exist
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
convert_LEVEL5_prism_to_gDR_input	load, convert and process the level 5 PRISM data into a gDR input
convert_LEVEL6_prism_to_gDR_input	load, convert and process the level 6 PRISM data into a gDR input
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
correct_template_sheets	Correct names of the template sheets (if required)
detect_file_format	Detect format of results data
enhance_raw_edited_EnVision_df	Enhance raw edited EnVision data.table
fix_typos_with_reference	Fix typos using reference data
gdr_test_data-class	gDR Test Data object
getPSet	Get PharmacoSet
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_EnVision_properties	Get properties of EnVision data
get_excel_sheet_names	get Excel sheets names for a charvec of files for non-Excel files return 0
get_exception_data	get exception data
get_expected_template_sheets	Get names of the sheets expected in templates xlsx
get_plate_info_from_template_xlsx	Get plate info from template xlsx
get_test_D300_data	get test D300 data
get_test_data	get primary test 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
get_xl_sheets	Get Excel sheets
import_D300	Import D300
is_readable_v	is_readable_v Check if all paths in vector are readable
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
manifest_path	Method manifest_path
manifest_path-method	Method manifest_path
mgrepl	grep wrapper to support multiple patterns
parse_D300_xml	Parse D300
read_EnVision_delim	Read EnVision delimited text files
read_EnVision_xlsx	Read in single xlsx data from EnVision
read_excel_to_dt	Read excel file and transorm it into data.table object
read_in_EnVision_file	Read EnVision file
read_in_manifest_file	read manifest files
read_in_results_Tecan	read in Tecan data
read_in_result_files	Read in results files
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
read_ref_data	read_ref_data
result_path	Method result_path
result_path-method	Method result_path
save_drug_info_per_well	for each drug create a Gnumber and Concentration information for each well
setEnvForPSet	Adjust environment variables to meet gDR standards
standardize_record_values	standardize_record_values
template_path	Method template_path
template_path-method	Method template_path
validate_template_xlsx	Validate template xlsx data