Get Tissue Site Detail

Retrieve all tissue site detail information in the database

GTEx Portal API documentation

Usage

get_tissue_site_detail(page = 0, itemsPerPage = 250)

Arguments

page

Integer (default = 0).

itemsPerPage

Integer (default = 250).

Value

A tibble

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_endpoints(), get_subject(), get_variant(), get_variant_by_location()

Examples

# \dontrun{
  # returns a tibble with one row per tissue
  get_tissue_site_detail()
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 54
#> # A tibble: 54 × 18
#>    tissueSiteDetailId  colorHex colorRgb datasetId eGeneCount expressedGeneCount
#>    <chr>               <chr>    <chr>    <chr>          <int>              <int>
#>  1 Adipose_Subcutaneo… FF6600   255,102… gtex_v8        15607              28830
#>  2 Adipose_Visceral_O… FFAA00   255,170… gtex_v8        12482              28881
#>  3 Adrenal_Gland       33DD33   51,221,… gtex_v8         8123              28235
#>  4 Artery_Aorta        FF5555   255,85,… gtex_v8        12493              28025
#>  5 Artery_Coronary     FFAA99   255,170… gtex_v8         6296              28462
#>  6 Artery_Tibial       FF0000   255,0,0  gtex_v8        15008              27217
#>  7 Bladder             AA0000   170,0,0  gtex_v8           NA              28949
#>  8 Brain_Amygdala      EEEE00   238,238… gtex_v8         3726              28196
#>  9 Brain_Anterior_cin… EEEE00   238,238… gtex_v8         5640              28921
#> 10 Brain_Caudate_basa… EEEE00   238,238… gtex_v8         8362              29230
#> # ℹ 44 more rows
#> # ℹ 12 more variables: hasEGenes <lgl>, hasSGenes <lgl>, mappedInHubmap <lgl>,
#> #   eqtlSampleSummary <list>, rnaSeqSampleSummary <list>, sGeneCount <int>,
#> #   samplingSite <chr>, tissueSite <chr>, tissueSiteDetail <chr>,
#> #   tissueSiteDetailAbbr <chr>, ontologyId <chr>, ontologyIri <chr>

  # `eqtlSampleSummary` and `rnaSeqSampleSummary` are list columns
  bladder_site_details <- get_tissue_site_detail() |>
    dplyr::filter(tissueSiteDetailId == "Bladder")
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 54

  purrr::pluck(bladder_site_details, "eqtlSampleSummary", 1)
#> $totalCount
#> [1] 21
#> 
#> $female
#> $female$ageMax
#> [1] 59
#> 
#> $female$ageMin
#> [1] 27
#> 
#> $female$ageMean
#> [1] 43.6
#> 
#> $female$count
#> [1] 7
#> 
#> 
#> $male
#> $male$ageMax
#> [1] 61
#> 
#> $male$ageMin
#> [1] 21
#> 
#> $male$ageMean
#> [1] 46
#> 
#> $male$count
#> [1] 14
#> 
#> 

  purrr::pluck(bladder_site_details, "rnaSeqSampleSummary", 1)
#> $totalCount
#> [1] 21
#> 
#> $female
#> $female$ageMax
#> [1] 59
#> 
#> $female$ageMin
#> [1] 27
#> 
#> $female$ageMean
#> [1] 43.6
#> 
#> $female$count
#> [1] 7
#> 
#> 
#> $male
#> $male$ageMax
#> [1] 61
#> 
#> $male$ageMin
#> [1] 21
#> 
#> $male$ageMean
#> [1] 46
#> 
#> $male$count
#> [1] 14
#> 
#> 
# }