gtexr (version 0.2.1)

get_significant_single_tissue_eqtls: Get Significant Single Tissue Eqtls

Description

Find significant single tissue eQTLs.

• This service returns precomputed significant single tissue eQTLs.

• Results may be filtered by tissue, gene, variant or dataset.

• To search by gene, use the versioned GENCODE ID.

• To search by variant, use the dbSNP rs ID (snpId).

By default, the service queries the latest GTEx release and the retrieved data is split into pages with items_per_page entries per page

GTEx Portal API documentation.

Usage

get_significant_single_tissue_eqtls(
  gencodeIds = NULL,
  variantIds = NULL,
  tissueSiteDetailIds = NULL,
  datasetId = "gtex_v8",
  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").

variantIds

Character vector. Gtex variant IDs.

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

Details

Note: although the GTEx Portal API documentation says to use the dbSNP rsID when searching by variant, this returns no results. Instead use gtex variant IDs e.g. use "chr1_153209640_C_A_b38" instead of "rs1410858".

See Also

Other Static Association Endpoints: get_eqtl_genes(), get_fine_mapping(), get_independent_eqtl(), get_multi_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_significant_single_tissue_eqtls(gencodeIds = c(
  "ENSG00000132693.12",
  "ENSG00000203782.5"
))

# search by variant - must be variantId (not rsid)
get_significant_single_tissue_eqtls(variantIds = "chr1_153209640_C_A_b38")

# filter by gene/variant and tissue site - either `gencodeIds` or `variantIds`
# should be supplied as a minimum
get_significant_single_tissue_eqtls(
  gencodeIds = c(
    "ENSG00000132693.12",
    "ENSG00000203782.5"
  ),
  variantIds = "chr1_153209640_C_A_b38",
  tissueSiteDetailIds = "Whole_Blood"
)
}