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Get Sample (Datasets Endpoints)

Source: R/get_sample_datasets_endpoints.R
get_sample_datasets_endpoints.Rd

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_endpoints(
  datasetId = "gtex_v8",
  sampleIds = NULL,
  tissueSampleIds = NULL,
  subjectIds = NULL,
  ageBrackets = NULL,
  sex = NULL,
  pathCategory = NULL,
  tissueSiteDetailId = NULL,
  aliquotIds = NULL,
  autolysisScores = NULL,
  hardyScales = NULL,
  ischemicTime = NULL,
  ischemicTimeGroups = NULL,
  rin = NULL,
  uberonIds = NULL,
  dataTypes = NULL,
  sortBy = NULL,
  sortDirection = NULL,
  page = NULL,
  itemsPerPage = NULL
)

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".

tissueSiteDetailId

String. The ID of the tissue of interest. Can be a GTEx specific ID (e.g. "Whole_Blood"; use get_tissue_site_detail() to see valid values) or an Ontology ID.

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".

ischemicTime

Integer.

ischemicTimeGroups

Character vector. Options: "<= 0", "1 - 300", "301 - 600", "601 - 900", "901 - 1200", "1201 - 1500", "> 1500".

rin

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).

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_subject(), get_tissue_site_detail(), get_variant(), get_variant_by_location()

Examples

# \dontrun{
 get_sample_datasets_endpoints()
#> Warning: ! Total number of items (22734) exceeds maximum page size (250).
#> ℹ Try increasing `itemsPerPage`.
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 91
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 22734
#> # A tibble: 10,946 × 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         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ  
#>  8         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ  
#>  9         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ  
#> 10         1214 SM-5GZZ7  GTEX-1117F-0226      Adipose - Subcutaneous   RNASEQ  
#> # ℹ 10,936 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 <chr>, pathologyNotesCategories <named list>,
#> #   pathologyNotes <chr>, autolysisScore <chr>
# }