gtexr (version 0.2.1)

get_sample_datasets: 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
)

Value

A tibble. Or a list if .return_raw = TRUE.

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

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

if (FALSE) { # identical(Sys.getenv("IN_PKGDOWN"), "true")
get_sample_datasets()
}