R: R Interface to European Genome-Phenome Archive

# R Interface to European Genome-Phenome Archive

## Documentation for package ‘Rega’ version 1.0.0

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

## Help Pages

add_required_str | Mark Required Fields with a Prefix
aliases_formatter | Format Aliases from a Table
api_function_factory | Generate an API Function from Operation and Specification
api_name_to_label | Convert API Names to Prettified Labels
column_table_formatter | Format a Column Table
create_client | Generate API Client Functions
default_parser | Parser for a Default EGA Excel Template
default_validator | Validator for Default Parser
delete_submission | Delete a Submission and Log Responses
delete_submission_contents | Delete Submission Contents and Log Responses
DELIM_CONVERTERS | Default Column Converters for EGA Metadata
ega_oauth | Set The OAUTH With EGA Username And Password
ega_token | Retrieve EGA API Bearer Token
extract_api | Extract API Specification and Host Details
extract_operation_definitions | Extract API Operation Definitions
extract_resource_name | Extract Resource Name from API Response URL
fetch_files | Fetch file information from EGA inbox
file_formatter | Format File Table with EGA File Paths
filter_id_fields | Filter Out ID Fields from a Character Vector
finalise_submission | Finalise an EGA submission
first_row_to_colnames | Use First Row as Column Names for a Data Frame
fold_column | Fold Columns with a Common Prefix into a Single Column Nested as List
format_chromosomes | Format Chromosome Metadata
get_chr_group | Retrieve Chromosome Belonging to a Group
get_entry_by_title | Retrieve EGA entries by title
get_enum | Retrieve Enum Values from an API
get_formatter | Retrieve a Formatter Function by Type of Submission Metadata Table
get_formatter_params | Retrieve Formatter Parameters by Name
get_operation_schema | Retrieve the Schema for an API Operation
get_or_post | Retrieve or Submit Data to an EGA API Endpoint
get_properties | Extract and Format Properties from a Schema
get_schemas | Retrieve Request schemas from an API Specification
get_sentence_number | Count the number of sentences in text
get_submission | Retrieve Submission Data and Log Responses
get_word_number | Count the number of words in text
has_linked_sheets | Check for Linked Sheets in Metadata
is_accession | Check if a String is a Valid Accession Identifier.
is_provisional | Check whether IDs is a provisional ID.
is_valid_http_method | Validate HTTP Method
label_to_api_name | Convert Prettified Labels to API Names
link_sheet | Link Data Between Metadata Sheets
lut_add | Add a Column to a Data Frame Based on Lookup Table
merge_linked_sheet | Merge Linked Sheets with Source Data
multi_lut_add | Add Multiple Lookup-Based Columns to a Data Frame
na_to_empty_list | Convert NA Values to Empty Lists
new_submission | Submit New Data to EGA
parse_ega_body | Parse The Information From EGA httr2 Response Object.
parse_enum | Parse Enum into a Formatted String
parse_json_body | Parse and Standardize JSON Response Body
parse_text_body | Parse Plain Text or JSON-like Response Body
process_chromosomes | Process a Vector or List of Chromosome Data
process_delimited_column | Process Delimited Columns in Metadata
rollback_submission | Rollback Submission Endpoints and Log Responses
row_table_formatter | Format a Row Table
samples_in_db | Check if sample aliases exist in the EGA database
save_log | Save API Responses to a Log File
step_msg | Generate a Step-by-Step Message Function
submit_table | Submit a Data Frame to an API Endpoint Row by Row
try_step | Execute a submission step with error handling and rollback
unbox_list | Convert a List to an Unboxed JSON-Compatible Data Frame
unbox_row | Convert a Data Frame Row to an Unboxed JSON Object
use_submission | Retrieve or Delete Submission Data
validate_schema | Validate a Payload Against a JSON Schema
validation_to_msg | Convert Validation Results to a Message
workflow_error_handler | Workflow Error Handler