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Get Sample (Biobank Data)

Source: R/get_sample_biobank_data.R
get_sample_biobank_data.Rd

GTEx Portal API documentation

Usage

get_sample_biobank_data(
  draw = NULL,
  materialTypes = NULL,
  tissueSiteDetailIds = NULL,
  pathCategory = NULL,
  tissueSampleIds = NULL,
  sex = NULL,
  sortBy = "sampleId",
  sortDirection = "asc",
  searchTerm = NULL,
  sampleIds = NULL,
  subjectIds = NULL,
  ageBrackets = NULL,
  hardyScales = NULL,
  hasExpressionData = NULL,
  hasGenotype = NULL,
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Arguments

draw

Integer.

materialTypes

String, vector. Options: "Cells:Cell Line Viable", "DNA:DNA Genomic", "DNA:DNA Somatic", "RNA:Total RNA", "Tissue:PAXgene Preserved", "Tissue:PAXgene Preserved Paraffin-embedded", "Tissue:Fresh Frozen Tissue".

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.

pathCategory

Character vector. Options: "adenoma", "amylacea", "atelectasis", "atherosclerosis", "atherosis", "atrophy", "calcification", "cirrhosis", "clean_specimens", "congestion", "corpora_albicantia", "cyst", "desquamation", "diabetic", "dysplasia", "edema", "emphysema", "esophagitis", "fibrosis", "gastritis", "glomerulosclerosis", "goiter", "gynecomastoid", "hashimoto", "heart_failure_cells", "hemorrhage", "hepatitis", "hyalinization", "hypereosinophilia", "hyperplasia", "hypertrophy", "hypoxic", "infarction", "inflammation", "ischemic_changes", "macrophages", "mastopathy", "metaplasia", "monckeberg", "necrosis", "nephritis", "nephrosclerosis", "no_abnormalities", "nodularity", "pancreatitis", "pigment", "pneumonia", "post_menopausal", "prostatitis", "saponification", "scarring", "sclerotic", "solar_elastosis", "spermatogenesis", "steatosis", "sweat_glands", "tma".

tissueSampleIds

Array of strings. A list of Tissue Sample ID(s).

sex

String. Options: "male", "female".

sortBy

String. Options: "sampleId", "ischemicTime", "aliquotId", "tissueSampleId", "hardyScale", "pathologyNotes", "ageBracket", "tissueSiteDetailId", "sex".

sortDirection

String. Options: "asc", "desc". Default = "asc".

searchTerm

String.

sampleIds

Character vector. GTEx sample ID.

subjectIds

Character vector. GTEx subject ID.

ageBrackets

The age bracket(s) of the donors of interest. Options: "20-29", "30-39", "40-49", "50-59", "60-69", "70-79".

hardyScales

Character vector. A list of Hardy Scale(s) of interest. Options: "Ventilator case", "Fast death - violent", "Fast death - natural causes", "Intermediate death", "Slow death".

hasExpressionData

Logical.

hasGenotype

Logical.

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 Biobank Data Endpoints: download()

Examples

get_sample_biobank_data(tissueSiteDetailIds = "Whole_Blood")
#> Warning: ! Total number of items (1388) exceeds the selected maximum page size (250).
#> ✖ 1138 items were not retrieved.
#> ℹ To retrieve all available items, increase `itemsPerPage`, ensuring you reuse
#>   your original query parameters e.g.
#>   `get_sample_biobank_data(<your_existing_parameters>, itemsPerPage = 100000)`
#> ℹ Alternatively, adjust global "gtexr.itemsPerPage" setting e.g.
#>   `options(list(gtexr.itemsPerPage = 100000))`
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 6
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems (recordsFiltered) = 1388
#> • recordsTotal = 75516
#> # A tibble: 250 × 26
#>    materialType    sampleId       sampleIdUpper sex   hasGTExImage concentration
#>    <chr>           <chr>          <chr>         <chr> <lgl>                <dbl>
#>  1 DNA:DNA Genomic GTEX-1117F-00… GTEX-1117F-0… fema… FALSE               125   
#>  2 DNA:DNA Genomic GTEX-1117F-00… GTEX-1117F-0… fema… FALSE               125   
#>  3 RNA:Total RNA   GTEX-1117F-00… GTEX-1117F-0… fema… FALSE               154   
#>  4 RNA:Total RNA   GTEX-1117F-00… GTEX-1117F-0… fema… FALSE                41.2 
#>  5 DNA:DNA Genomic GTEX-111CU-00… GTEX-111CU-0… male  FALSE                85.9 
#>  6 RNA:Total RNA   GTEX-111CU-00… GTEX-111CU-0… male  FALSE                96.0 
#>  7 RNA:Total RNA   GTEX-111CU-00… GTEX-111CU-0… male  FALSE                96.0 
#>  8 RNA:Total RNA   GTEX-111CU-00… GTEX-111CU-0… male  FALSE                95.3 
#>  9 DNA:DNA Genomic GTEX-111FC-00… GTEX-111FC-0… male  FALSE               125   
#> 10 DNA:DNA Genomic GTEX-111FC-00… GTEX-111FC-0… male  FALSE                 4.35
#> # ℹ 240 more rows
#> # ℹ 20 more variables: analysisRelease <chr>, genotype <chr>, hardyScale <chr>,
#> #   pathologyNotes <chr>, subjectId <chr>, tissueSiteDetailId <chr>,
#> #   hasGenotype <lgl>, originalMaterialType <chr>, aliquotId <chr>,
#> #   tissueSampleId <chr>, ageBracket <chr>, brainTissueDonor <lgl>,
#> #   volume <dbl>, hasExpressionData <lgl>, hasBRDImage <lgl>,
#> #   tissueSiteDetail <chr>, amount <dbl>, mass <dbl>, tissueSite <chr>, …