get_significant_single_tissue_eqtls: Get Significant Single Tissue Eqtls

In gtexr: Query the GTEx Portal API

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 = 250
)

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).

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".

Value

A tibble.

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

## Not run: 
# 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")

## End(Not run)

gtexr documentation built on Sept. 19, 2024, 5:06 p.m.