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Get Significant Single Tissue Ieqtls

Source: R/get_significant_single_tissue_ieqtls.R
get_significant_single_tissue_ieqtls.Rd

Retrieve Interaction eQTL Data.

  • This service returns cell type interaction eQTLs (ieQTLs), 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_ieqtls(
  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_isqtls(), get_significant_single_tissue_sqtls(), get_sqtl_genes()

Examples

# \dontrun{
get_significant_single_tissue_ieqtls(c("ENSG00000132693.12",
                                       "ENSG00000203782.5"))
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 86
#> # A tibble: 86 × 24
#>    snpId     bGISE    pos snpIdUpper pValueG pValueGI geneSymbol geneSymbolUpper
#>    <chr>     <dbl>  <int> <chr>        <dbl>    <dbl> <chr>      <chr>          
#>  1 rs34188… 0.0890 1.54e8 RS34188388  0.102  0.00447  LOR        LOR            
#>  2 rs24945… 0.0654 1.60e8 RS2494523   0.867  0.00129  CRP        CRP            
#>  3 rs986760 0.148  1.53e8 RS986760    0.0454 0.00694  LOR        LOR            
#>  4 rs17697… 0.0428 1.59e8 RS17697329  0.515  0.000627 CRP        CRP            
#>  5 rs67415… 0.154  1.53e8 RS67415955  0.565  0.000754 LOR        LOR            
#>  6 rs12133… 0.157  1.60e8 RS12133356  0.634  0.00106  CRP        CRP            
#>  7 rs12132… 0.113  1.53e8 RS12132927  0.858  0.00365  LOR        LOR            
#>  8 rs30269… 0.0683 1.59e8 RS3026943   0.684  0.00222  CRP        CRP            
#>  9 rs24946… 0.0567 1.54e8 RS2494670   0.516  0.000595 LOR        LOR            
#> 10 rs12121… 0.0695 1.60e8 RS12121609  0.444  0.000266 CRP        CRP            
#> # ℹ 76 more rows
#> # ℹ 16 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>
# }