gtexr (version 0.2.1)

get_tissue_site_detail: Get Tissue Site Detail

Description

Retrieve all tissue site detail information in the database

GTEx Portal API documentation

Usage

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

Value

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

Arguments

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

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_linkage_disequilibrium_data(), get_sample_datasets(), get_subject(), get_variant(), get_variant_by_location()

Examples

if (FALSE) { # identical(Sys.getenv("IN_PKGDOWN"), "true")
# returns a tibble with one row per tissue
get_tissue_site_detail()

# `eqtlSampleSummary` and `rnaSeqSampleSummary` are list columns
bladder_site_details <- get_tissue_site_detail() |>
  dplyr::filter(tissueSiteDetailId == "Bladder")

purrr::pluck(bladder_site_details, "eqtlSampleSummary", 1)

purrr::pluck(bladder_site_details, "rnaSeqSampleSummary", 1)
}