gtexr (version 0.2.1)

get_fine_mapping: Get Fine Mapping

Description

Retrieve Fine Mapping Data

• Finds and returns Fine Mapping 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_fine_mapping(
  gencodeIds,
  datasetId = "gtex_v8",
  variantId = NULL,
  tissueSiteDetailIds = NULL,
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Value

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

Arguments

gencodeIds

A character vector of Versioned GENCODE IDs, e.g. c("ENSG00000132693.12", "ENSG00000203782.5").

datasetId

String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot".

variantId

String. A gtex variant ID.

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.

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

See Also

Other Static Association Endpoints: get_eqtl_genes(), get_independent_eqtl(), 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

if (FALSE) { # identical(Sys.getenv("IN_PKGDOWN"), "true")
# search by gene
get_fine_mapping(gencodeIds = c(
  "ENSG00000132693.12",
  "ENSG00000203782.5"
))

# optionally filter for a single variant and/or one or more tissues
get_fine_mapping(
  gencodeIds = c(
    "ENSG00000132693.12",
    "ENSG00000203782.5"
  ),
  variantId = "chr1_153228363_A_G_b38",
  tissueSiteDetailIds = c(
    "Whole_Blood",
    "Thyroid"
  )
)
}