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Get Linkage Disequilibrium By Variant Data

Source: R/get_linkage_disequilibrium_by_variant_data.R
get_linkage_disequilibrium_by_variant_data.Rd

Find linkage disequilibrium (LD) data for a given variant

GTEx Portal API documentation

Usage

get_linkage_disequilibrium_by_variant_data(
  variantId,
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Arguments

variantId

String. A gtex variant ID.

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_data(), get_sample_datasets(), get_subject(), get_tissue_site_detail(), get_variant(), get_variant_by_location()

Examples

get_linkage_disequilibrium_by_variant_data("chr1_159245536_C_T_b38")
#> Warning: ! Total number of items (503) exceeds the selected maximum page size (250).
#> ✖ 253 items were not retrieved.
#> ℹ To retrieve all available items, increase `itemsPerPage`, ensuring you reuse
#>   your original query parameters e.g.
#>   `get_linkage_disequilibrium_by_variant_data(<your_existing_parameters>,
#>   itemsPerPage = 100000)`
#> ℹ Alternatively, adjust global "gtexr.itemsPerPage" setting e.g.
#>   `options(list(gtexr.itemsPerPage = 100000))`
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 3
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 503
#> # A tibble: 250 × 3
#>    variantId_1             variantId_2               ld
#>    <chr>                   <chr>                  <dbl>
#>  1 chr1_159163610_GA_G_b38 chr1_159245536_C_T_b38 0.114
#>  2 chr1_159163924_G_A_b38  chr1_159245536_C_T_b38 0.114
#>  3 chr1_159164864_T_C_b38  chr1_159245536_C_T_b38 0.114
#>  4 chr1_159165054_A_G_b38  chr1_159245536_C_T_b38 0.113
#>  5 chr1_159165563_T_C_b38  chr1_159245536_C_T_b38 0.113
#>  6 chr1_159174791_T_C_b38  chr1_159245536_C_T_b38 0.252
#>  7 chr1_159176518_G_T_b38  chr1_159245536_C_T_b38 0.146
#>  8 chr1_159176900_C_A_b38  chr1_159245536_C_T_b38 0.271
#>  9 chr1_159177147_A_T_b38  chr1_159245536_C_T_b38 0.274
#> 10 chr1_159179691_T_C_b38  chr1_159245536_C_T_b38 0.253
#> # ℹ 240 more rows