get_sample_datasets: Get Sample (Datasets)

In gtexr: Query the GTEx Portal API

Get Sample (Datasets)

Description

This service returns information of samples used in analyses from all datasets. Results may be filtered by dataset ID, sample ID, subject ID, sample metadata, or other provided parameters. By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_sample_datasets(
  datasetId = "gtex_v8",
  sampleIds = NULL,
  tissueSampleIds = NULL,
  subjectIds = NULL,
  ageBrackets = NULL,
  sex = NULL,
  pathCategory = NULL,
  tissueSiteDetailIds = NULL,
  aliquotIds = NULL,
  autolysisScores = NULL,
  hardyScales = NULL,
  ischemicTimes = NULL,
  ischemicTimeGroups = NULL,
  rins = NULL,
  uberonIds = NULL,
  dataTypes = NULL,
  sortBy = "sampleId",
  sortDirection = "asc",
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Arguments

datasetId	String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot".
sampleIds	Character vector. GTEx sample ID.
tissueSampleIds	Array of strings. A list of Tissue Sample ID(s).
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".
sex	String. Options: "male", "female".
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".
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.
aliquotIds	Character vector.
autolysisScores	Character vector. Options: "None", "Mild", "Moderate", "Severe".
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".
ischemicTimes	Integer.
ischemicTimeGroups	Character vector. Options: "<= 0", "1 - 300", "301 - 600", "601 - 900", "901 - 1200", "1201 - 1500", "> 1500".
rins	Integer, vector.
uberonIds	Character vector of Uberon IDs (e.g. "UBERON:EFO_0000572"; use get_tissue_site_detail() to see valid values).
dataTypes	Character vector. Options: "RNASEQ", "WGS", "WES", "OMNI", "EXCLUDE".
sortBy	String. Options: "sampleId", "ischemicTime", "aliquotId", "tissueSampleId", "hardyScale", "pathologyNotes", "ageBracket", "tissueSiteDetailId", "sex".
sortDirection	String. Options: "asc", "desc". Default = "asc".
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_linkage_disequilibrium_data(), get_subject(), get_tissue_site_detail(), get_variant(), get_variant_by_location()

Examples

## Not run: 
get_sample_datasets()

## End(Not run)

gtexr documentation built on June 8, 2025, 10:26 a.m.