get_sample_datasets {gtexr} | R Documentation |
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.
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
|
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 |
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 |
.verbose |
Logical. If |
.return_raw |
Logical. If |
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)