Developer guide

Functions

Function name is title of API endpoint in lower case, with words separated by underscores.
@description section is copied verbatim from the API documentation site and ends with a link to the corresponding API endpoint documentation.
Further notes may be added under @details.
Arguments
- Names match those for API endpoint,¹ except where the argument accepts an array (vector in R) of values, in which case it is pluralised.²
- Default values also match those for API endpoint.
- Query parameters flagged as “required” in the GTEx Portal API documentation do not have default values.³
- Are all documented in gtexr_arguments.R. All functions therefore use @inheritParams gtexr_arguments for documentation.
- All have a .return_raw argument (default value FALSE), allowing users to retrieve the raw JSON from an API call.
- Functions which return a paginated response should have a .verbose argument (default value getOption("gtexr.verbose"), which is set to TRUE) and set argument itemsPerPage to getOption("gtexr.itemsPerPage") (which is set to 250 by default).
Use @family roxygen tag to match categories on API documentation. This is used to categorise functions on pkgdown site reference page.
Return a tibble.
The first example in @examples must produce output and be a single function call without assignment (e.g. get_news_items(), not x <- get_news_items()). This is used to pre-populate argument values in the gtexr shiny app with a working example.
All examples should be surrounded by \dontrun{}.

Note that the Get Genomic Features endpoint takes a path parameter “featureId”, for which the corresponding gtexr argument is prefixed with “.” (.featureId).↩︎
The parameter pathCategory always accepts an array however, and is therefore not pluralised.↩︎
Note however that while variantId is not flagged as “required” for Get Linkage Disequilibrium By Variant Data, no default value is provided in get_linkage_disequilibrium_by_variant_data() as providing NULL or an unrecognised variant ID returns an empty response.↩︎