get_independent_eqtl: Get Independent Eqtl

In gtexr: Query the GTEx Portal API

Get Independent Eqtl

Description

Retrieve Independent eQTL Data

• Finds and returns ⁠Independent eQTL Data⁠ data for the provided list of genes

• By default, this endpoint fetches data from the latest GTEx version

The retrieved data is split into pages with items_per_page entries per page

GTEx portal API documentation

Usage

get_independent_eqtl(
  gencodeIds,
  tissueSiteDetailIds = NULL,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Arguments

gencodeIds	A character vector of Versioned GENCODE IDs, e.g. c("ENSG00000132693.12", "ENSG00000203782.5").
tissueSiteDetailIds	Character vector of IDs for tissues of interest. Can be GTEx specific IDs (e.g. "Whole_Blood"; use get_tissue_site_detail() to see valid values) or Ontology IDs.
datasetId	String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot".
page	Integer (default = 0).
itemsPerPage	Integer (default = 250). Set globally to maximum value 100000 with options(list(gtexr.itemsPerPage = 100000)).
.verbose	Logical. If TRUE (default), print paging information. Set to FALSE globally with options(list(gtexr.verbose = FALSE)).
.return_raw	Logical. If TRUE, return the raw API JSON response. Default = FALSE

Value

A tibble. Or a list if .return_raw = TRUE.

See Also

Other Static Association Endpoints: get_eqtl_genes(), get_fine_mapping(), get_multi_tissue_eqtls(), get_significant_single_tissue_eqtls(), get_significant_single_tissue_eqtls_by_location(), get_significant_single_tissue_ieqtls(), get_significant_single_tissue_isqtls(), get_significant_single_tissue_sqtls(), get_sqtl_genes()

Examples

## Not run: 
# search by gene
get_independent_eqtl(gencodeIds = c(
  "ENSG00000132693.12",
  "ENSG00000203782.5"
))

# optionally filter for a single variant and/or one or more tissues
get_independent_eqtl(
  gencodeIds = c(
    "ENSG00000132693.12",
    "ENSG00000203782.5"
  ),
  tissueSiteDetailIds = c(
    "Whole_Blood",
    "Thyroid"
  )
)

## End(Not run)

gtexr documentation built on June 8, 2025, 10:26 a.m.