Developer guide
In gtexr: Query the GTEx Portal API

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

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, except where the argument accepts an array (vector in R) of values, in which case it is pluralised.[^1]
- Default values also match those for API endpoint.
- Query parameters flagged as "required" in the GTEx Portal API documentation do not have default values.[^2]
- Are all documented in gtexr_arguments.R. All functions therefore use @inheritParams gtexr_arguments for documentation.
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{}.

[^1]: Note that the Get Genomic Features endpoint takes a path parameter "featureId". The corresponding gtexr argument is prefixed with "." (.featureId).

[^2]: 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.