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Get Linkage Disequilibrium Data

Source: R/get_linkage_disequilibrium_data.R
get_linkage_disequilibrium_data.Rd

Find linkage disequilibrium (LD) data for a given gene.

This endpoint returns linkage disequilibrium data for the cis-eQTLs found associated with the provided gene in a specified dataset. Results are queried by gencode ID. By default, the service queries the latest GTEx release. Specify a dataset ID to fetch results from a different dataset.

GTEx Portal API documentation

Usage

get_linkage_disequilibrium_data(
  gencodeId,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Arguments

gencodeId

String. A Versioned GENCODE ID of a gene, e.g. "ENSG00000065613.9".

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). Set globally to maximum value 100000 with options(list(gtexr.itemsPerPage = 100000)).

.verbose

Logical. If TRUE (default), print paging information. Set to FALSE globally with options(list(gtexr.verbose = FALSE)).

.return_raw

Logical. If TRUE, return the raw API JSON response. Default = FALSE

Value

A tibble. Or a list if .return_raw = TRUE.

See also

Other Datasets Endpoints: get_annotation(), get_collapsed_gene_model_exon(), get_downloads_page_data(), get_file_list(), get_full_get_collapsed_gene_model_exon(), get_functional_annotation(), get_linkage_disequilibrium_by_variant_data(), get_sample_datasets(), get_subject(), get_tissue_site_detail(), get_variant(), get_variant_by_location()

Examples

get_linkage_disequilibrium_data(gencodeId = "ENSG00000132693.12")
#> Warning: ! Total number of items (3558) exceeds the selected maximum page size (250).
#> ✖ 3308 items were not retrieved.
#> ℹ To retrieve all available items, increase `itemsPerPage`, ensuring you reuse
#>   your original query parameters e.g.
#>   `get_linkage_disequilibrium_data(<your_existing_parameters>, itemsPerPage =
#>   100000)`
#> ℹ Alternatively, adjust global "gtexr.itemsPerPage" setting e.g.
#>   `options(list(gtexr.itemsPerPage = 100000))`
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 15
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 3558
#> # A tibble: 250 × 3
#>    variantId_1            variantId_2                         ld
#>    <chr>                  <chr>                            <dbl>
#>  1 chr1_159230230_G_T_b38 chr1_159230339_A_C_b38           1    
#>  2 chr1_159230230_G_T_b38 chr1_159245536_C_T_b38           0.971
#>  3 chr1_159230230_G_T_b38 chr1_159302270_T_C_b38           0.717
#>  4 chr1_159230230_G_T_b38 chr1_159343657_A_T_b38           0.302
#>  5 chr1_159230230_G_T_b38 chr1_159344052_G_A_b38           0.300
#>  6 chr1_159230230_G_T_b38 chr1_159347493_G_A_b38           0.300
#>  7 chr1_159230230_G_T_b38 chr1_159350390_C_A_b38           0.300
#>  8 chr1_159230230_G_T_b38 chr1_159351189_G_A_b38           0.300
#>  9 chr1_159230230_G_T_b38 chr1_159359256_C_A_b38           0.302
#> 10 chr1_159230230_G_T_b38 chr1_159360755_ATACATAAGTG_A_b38 0.300
#> # ℹ 240 more rows