View source: R/get_sample_biobank_data.R
get_sample_biobank_data | R Documentation |
get_sample_biobank_data(
draw = NULL,
materialTypes = NULL,
tissueSiteDetailIds = NULL,
pathCategory = NULL,
tissueSampleIds = NULL,
sex = NULL,
sortBy = "sampleId",
sortDirection = "asc",
searchTerm = NULL,
sampleIds = NULL,
subjectIds = NULL,
ageBrackets = NULL,
hardyScales = NULL,
hasExpressionData = NULL,
hasGenotype = NULL,
page = 0,
itemsPerPage = 250
)
draw |
Integer. |
materialTypes |
String, vector. Options: "Cells:Cell Line Viable", "DNA:DNA Genomic", "DNA:DNA Somatic", "RNA:Total RNA", "Tissue:PAXgene Preserved", "Tissue:PAXgene Preserved Paraffin-embedded", "Tissue:Fresh Frozen Tissue". |
tissueSiteDetailIds |
Character vector of IDs for tissues of interest.
Can be GTEx specific IDs (e.g. "Whole_Blood"; use
|
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". |
tissueSampleIds |
Array of strings. A list of Tissue Sample ID(s). |
sex |
String. Options: "male", "female". |
sortBy |
String. Options: "sampleId", "ischemicTime", "aliquotId", "tissueSampleId", "hardyScale", "pathologyNotes", "ageBracket", "tissueSiteDetailId", "sex". |
sortDirection |
String. Options: "asc", "desc". Default = "asc". |
searchTerm |
String. |
sampleIds |
Character vector. GTEx sample ID. |
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". |
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". |
hasExpressionData |
Logical. |
hasGenotype |
Logical. |
page |
Integer (default = 0). |
itemsPerPage |
Integer (default = 250). |
A tibble
Other Biobank Data Endpoints:
download()
## Not run:
get_sample_biobank_data(tissueSiteDetailIds = "Whole_Blood")
## End(Not run)
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