View source: R/gtexr_arguments.R
gtexr_arguments | R Documentation |
Internal function that documents all arguments for exported gtexr functions
that wrap GTEx Portal API endpoints (using roxygen @inheritParams
tag).
gtexr_arguments(
ageBrackets = NULL,
aliquotIds = NULL,
attributeSubset = NULL,
autolysisScores = NULL,
cellType = NULL,
bp_window = NULL,
chromosome = NULL,
datasetId = NULL,
dataTypes = NULL,
draw = NULL,
end = NULL,
excludeDataArray = NULL,
.featureId = NULL,
filterMtGene = NULL,
gencodeId = NULL,
gencodeIds = NULL,
gencodeVersion = NULL,
geneId = NULL,
geneIds = NULL,
genomeBuild = NULL,
hardyScales = NULL,
hasExpressionData = NULL,
hasGenotype = NULL,
itemsPerPage = NULL,
ischemicTime = NULL,
ischemicTimeGroups = NULL,
materialTypes = NULL,
organizationName = NULL,
page = NULL,
pathCategory = NULL,
phenotypeId = NULL,
pos = NULL,
project_id = NULL,
rin = NULL,
sampleId = NULL,
sampleIds = NULL,
searchTerm = NULL,
sex = NULL,
snpId = NULL,
sortBy = NULL,
sortDirection = NULL,
start = NULL,
subjectIds = NULL,
tissueSampleIds = NULL,
tissueSiteDetailId = NULL,
tissueSiteDetailIds = NULL,
uberonIds = NULL,
variantId = NULL,
variantIds = NULL
)
ageBrackets |
The age bracket(s) of the donors of interest. Options: "20-29", "30-39", "40-49", "50-59", "60-69", "70-79". |
aliquotIds |
Character vector. |
attributeSubset |
String. Examples include but are not limited to "sex", "ageBracket" |
autolysisScores |
Character vector. Options: "None", "Mild", "Moderate", "Severe". |
cellType |
String. "Adipocytes", "Epithelial_cells", "Hepatocytes", "Keratinocytes", "Myocytes", "Neurons", "Neutrophils". |
bp_window |
Integer. |
chromosome |
String. One of "chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrM", "chrX", "chrY". |
datasetId |
String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot". |
dataTypes |
Character vector. Options: "RNASEQ", "WGS", "WES", "OMNI", "EXCLUDE". |
draw |
Integer. |
end |
Integer. |
excludeDataArray |
String. Options are TRUE or FALSE |
.featureId |
String. A genomic feature e.g. GENCODE ID, RSID or GTEx Variant ID. |
filterMtGene |
Logical. Exclude mitochondrial genes. |
gencodeId |
String. A Versioned GENCODE ID of a gene, e.g. "ENSG00000065613.9". |
gencodeIds |
A character vector of Versioned GENCODE IDs, e.g. c("ENSG00000132693.12", "ENSG00000203782.5"). |
gencodeVersion |
String (default = "v26"). GENCODE annotation release. Either "v26" or "v19". |
geneId |
String. A gene symbol, a gencode ID, or an Ensemble ID. |
geneIds |
A character vector of gene symbols, versioned gencodeIds, or unversioned gencodeIds. |
genomeBuild |
String. Options: "GRCh38/hg38", "GRCh37/hg19". Default = "GRCh38/hg38". |
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. |
itemsPerPage |
Integer (default = 250). |
ischemicTime |
Integer. |
ischemicTimeGroups |
Character vector. Options: "<= 0", "1 - 300", "301 - 600", "601 - 900", "901 - 1200", "1201 - 1500", "> 1500". |
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". |
organizationName |
String. Options: "GTEx Consortium" "Kid's First". |
page |
Integer (default = 0). |
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". |
phenotypeId |
String. See GTEx portal FAQs for further details. |
pos |
Integer, vector. |
project_id |
String. Options: "gtex", "adult-gtex", "egtex". |
rin |
Integer vector. |
sampleId |
String. |
sampleIds |
Character vector. GTEx sample ID. |
searchTerm |
String. |
sex |
String. Options: "male", "female". |
snpId |
String |
sortBy |
String. Options: "sampleId", "ischemicTime", "aliquotId", "tissueSampleId", "hardyScale", "pathologyNotes", "ageBracket", "tissueSiteDetailId", "sex". |
sortDirection |
String. Options: "asc", "desc". Default = "asc". |
start |
Integer. |
subjectIds |
Character vector. GTEx subject ID. |
tissueSampleIds |
Array of strings. A list of Tissue Sample ID(s). |
tissueSiteDetailId |
String. The ID of the tissue of interest. Can be a
GTEx specific ID (e.g. "Whole_Blood"; use |
tissueSiteDetailIds |
Character vector of IDs for tissues of interest.
Can be GTEx specific IDs (e.g. "Whole_Blood"; use
|
uberonIds |
Character vector of Uberon IDs (e.g. "UBERON:EFO_0000572";
use |
variantId |
String. A gtex variant ID. |
variantIds |
Character vector. Gtex variant IDs. |
Returns NULL
invisibly. Used for documentation only.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.