Get Significant Single Tissue Sqtls
Source:R/get_significant_single_tissue_sqtls.R
get_significant_single_tissue_sqtls.Rd
Retrieve Single Tissue sQTL Data.
This service returns single tissue sQTL data for the given genes, from a specified dataset.
Results may be filtered by tissue
By default, the service queries the latest GTEx release.
The retrieved data is split into pages with items_per_page
entries per page
Usage
get_significant_single_tissue_sqtls(
gencodeIds,
variantIds = NULL,
tissueSiteDetailIds = NULL,
datasetId = "gtex_v8"
)
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".
See also
Other Static Association Endpoints:
get_eqtl_genes()
,
get_fine_mapping()
,
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_sqtl_genes()
Examples
# \dontrun{
# search by gene
get_significant_single_tissue_sqtls(gencodeIds = c("ENSG00000065613.9",
"ENSG00000203782.5"))
#>
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 176
#> # A tibble: 176 × 14
#> snpId pos snpIdUpper variantId geneSymbol pValue geneSymbolUpper
#> <chr> <int> <chr> <chr> <chr> <dbl> <chr>
#> 1 rs4636462 152442732 RS4636462 chr1_1524… LOR 7.71e-5 LOR
#> 2 rs4845768 152442997 RS4845768 chr1_1524… LOR 6.57e-5 LOR
#> 3 rs12069640 152444300 RS12069640 chr1_1524… LOR 7.13e-5 LOR
#> 4 rs11803629 152445670 RS11803629 chr1_1524… LOR 1.81e-4 LOR
#> 5 rs12125681 152445737 RS12125681 chr1_1524… LOR 1.81e-4 LOR
#> 6 rs11205004 152446586 RS11205004 chr1_1524… LOR 1.81e-4 LOR
#> 7 rs11579085 152447965 RS11579085 chr1_1524… LOR 1.81e-4 LOR
#> 8 rs1885529 152448570 RS1885529 chr1_1524… LOR 1.81e-4 LOR
#> 9 rs1885528 152448978 RS1885528 chr1_1524… LOR 1.81e-4 LOR
#> 10 rs1885527 152449069 RS1885527 chr1_1524… LOR 1.81e-4 LOR
#> # ℹ 166 more rows
#> # ℹ 7 more variables: datasetId <chr>, tissueSiteDetailId <chr>,
#> # ontologyId <chr>, chromosome <chr>, gencodeId <chr>, nes <dbl>,
#> # phenotypeId <chr>
# }