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.
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 toFALSEglobally withoptions(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_subject(),
get_tissue_site_detail(),
get_variant(),
get_variant_by_location()
Examples
get_sample_datasets()
#> Warning: ! Total number of items (22734) exceeds the selected maximum page size (250).
#> ✖ 22484 items were not retrieved.
#> ℹ To retrieve all available items, increase `itemsPerPage`, ensuring you reuse
#> your original query parameters e.g.
#> `get_sample_datasets(<your_existing_parameters>, itemsPerPage = 100000)`
#> ℹ Alternatively, adjust global "gtexr.itemsPerPage" setting e.g.
#> `options(list(gtexr.itemsPerPage = 100000))`
#>
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 91
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 22734
#> # A tibble: 250 × 20
#> ischemicTime aliquotId tissueSampleId tissueSiteDetail dataType
#> <int> <chr> <chr> <chr> <chr>
#> 1 1188 SM-58Q7G GTEX-1117F-0003 Whole Blood WES
#> 2 1188 SM-5DWSB GTEX-1117F-0003 Whole Blood OMNI
#> 3 1188 SM-6WBT7 GTEX-1117F-0003 Whole Blood WGS
#> 4 1193 SM-AHZ7F GTEX-1117F-0011-R10a Brain - Frontal Cortex … NA
#> 5 1193 SM-CYKQ8 GTEX-1117F-0011-R10b Brain - Frontal Cortex … NA
#> 6 1214 SM-5GZZ7 GTEX-1117F-0226 Adipose - Subcutaneous RNASEQ
#> 7 1220 SM-5EGHI GTEX-1117F-0426 Muscle - Skeletal RNASEQ
#> 8 1221 SM-5EGHJ GTEX-1117F-0526 Artery - Tibial RNASEQ
#> 9 1243 SM-5N9CS GTEX-1117F-0626 Artery - Coronary RNASEQ
#> 10 1244 SM-5GIEN GTEX-1117F-0726 Heart - Atrial Appendage RNASEQ
#> # ℹ 240 more rows
#> # ℹ 15 more variables: ischemicTimeGroup <chr>, freezeType <chr>,
#> # sampleId <chr>, sampleIdUpper <chr>, ageBracket <chr>, hardyScale <chr>,
#> # tissueSiteDetailId <chr>, subjectId <chr>, uberonId <chr>, sex <chr>,
#> # datasetId <chr>, rin <dbl>, pathologyNotesCategories <tibble[,57]>,
#> # pathologyNotes <chr>, autolysisScore <chr>