get_significant_single_tissue_eqtls {gtexr} | R Documentation |
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
|
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)