# Package for handling the import of dose-response data

## Documentation for package ‘gDRimport’ version 1.0.0

- 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_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_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