R Interface to European Genome-Phenome Archive

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Documentation for package ‘Rega’ version 0.99.6

• 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