Skip to contents

et Significant Single Tissue Isqtls

Source: R/get_significant_single_tissue_isqtls.R
get_significant_single_tissue_isqtls.Rd

Retrieve Interaction sQTL Data.

  • This service retrieves cell type interaction sQTLs (isQTLs), 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

GTEx Portal API documentation.

Usage

get_significant_single_tissue_isqtls(
  gencodeIds,
  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).

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(), get_significant_single_tissue_eqtls_by_location(), get_significant_single_tissue_ieqtls(), get_significant_single_tissue_sqtls(), get_sqtl_genes()

Examples

# \dontrun{
get_significant_single_tissue_isqtls(gencodeIds = c("ENSG00000065613.9",
                                                    "ENSG00000203782.5"))
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 4
#> # A tibble: 4 × 25
#>   snpId      bGISE    pos snpIdUpper pValueG pValueGI geneSymbol geneSymbolUpper
#>   <chr>      <dbl>  <int> <chr>        <dbl>    <dbl> <chr>      <chr>          
#> 1 rs4845790 0.0194 1.53e8 RS4845790  0.00645  8.97e-7 LOR        LOR            
#> 2 rs4845790 0.0196 1.53e8 RS4845790  0.0118   1.41e-7 LOR        LOR            
#> 3 rs359327… 0.0289 1.54e8 RS35932716 0.0142   3.70e-5 LOR        LOR            
#> 4 rs146285… 0.0293 1.53e8 RS1462851… 0.0225   3.03e-5 LOR        LOR            
#> # ℹ 17 more variables: pValueI <dbl>, bGI <dbl>, tissueSiteDetailId <chr>,
#> #   ontologyId <chr>, chromosome <chr>, tissueCellType <chr>,
#> #   tssDistance <int>, bGSE <dbl>, variantId <chr>, maf <dbl>, bISE <dbl>,
#> #   datasetId <chr>, bG <dbl>, pValueAdjustedBH <dbl>, bI <dbl>,
#> #   gencodeId <chr>, phenotypeId <chr>
# }