Get Fine Mapping

Retrieve Fine Mapping Data

• Finds and returns Fine Mapping data for the provided list of genes

• By default, this endpoint fetches data from the latest GTEx version

The retrieved data is split into pages with items_per_page entries per page

GTEx Portal API documentation

Usage

get_fine_mapping(
  gencodeIds,
  datasetId = "gtex_v8",
  variantId = NULL,
  tissueSiteDetailIds = NULL,
  page = 0,
  itemsPerPage = 250
)

Arguments

gencodeIds

A character vector of Versioned GENCODE IDs, e.g. c("ENSG00000132693.12", "ENSG00000203782.5").

datasetId

String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot".

variantId

String. A gtex variant ID.

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.

page

Integer (default = 0).

itemsPerPage

Integer (default = 250).

Value

A tibble.

See also

Other Static Association Endpoints: get_eqtl_genes(), 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_significant_single_tissue_sqtls(), get_sqtl_genes()

Examples

# \dontrun{
# search by gene
get_fine_mapping(gencodeIds = c("ENSG00000132693.12",
                               "ENSG00000203782.5"))
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 27
#> # A tibble: 27 × 9
#>    datasetId gencodeId          method     pip setId setSize tissueSiteDetailId
#>    <chr>     <chr>              <chr>    <dbl> <int>   <int> <chr>             
#>  1 gtex_v8   ENSG00000132693.12 DAP-G  0.0235      1       5 Thyroid           
#>  2 gtex_v8   ENSG00000132693.12 DAP-G  0.0221      1       5 Thyroid           
#>  3 gtex_v8   ENSG00000132693.12 DAP-G  0.0171      1       5 Thyroid           
#>  4 gtex_v8   ENSG00000132693.12 DAP-G  0.0252      1       5 Thyroid           
#>  5 gtex_v8   ENSG00000132693.12 DAP-G  0.892       1       5 Thyroid           
#>  6 gtex_v8   ENSG00000203782.5  DAP-G  0.0126      1      22 Whole_Blood       
#>  7 gtex_v8   ENSG00000203782.5  DAP-G  0.00690     1      22 Whole_Blood       
#>  8 gtex_v8   ENSG00000203782.5  DAP-G  0.0313      1      22 Whole_Blood       
#>  9 gtex_v8   ENSG00000203782.5  DAP-G  0.00852     1      22 Whole_Blood       
#> 10 gtex_v8   ENSG00000203782.5  DAP-G  0.0105      1      22 Whole_Blood       
#> # ℹ 17 more rows
#> # ℹ 2 more variables: ontologyId <chr>, variantId <chr>

# optionally filter for a single variant and/or one or more tissues
get_fine_mapping(gencodeIds = c("ENSG00000132693.12",
                               "ENSG00000203782.5"),
                 variantId = "chr1_153228363_A_G_b38",
                 tissueSiteDetailIds = c("Whole_Blood",
                                        "Thyroid"))
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 1
#> # A tibble: 1 × 9
#>   datasetId gencodeId  method    pip setId setSize tissueSiteDetailId ontologyId
#>   <chr>     <chr>      <chr>   <dbl> <int>   <int> <chr>              <chr>     
#> 1 gtex_v8   ENSG00000… DAP-G  0.0126     1      22 Whole_Blood        UBERON:00…
#> # ℹ 1 more variable: variantId <chr>
# }