gtexr_arguments: gtexr arguments

Description

Internal function that documents all arguments for exported gtexr functions that wrap GTEx Portal API endpoints (using roxygen @inheritParams tag).

Usage

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,
  hardyScale = NULL,
  hardyScales = NULL,
  hasExpressionData = NULL,
  hasGenotype = NULL,
  itemsPerPage = NULL,
  ischemicTimes = NULL,
  ischemicTimeGroups = NULL,
  materialTypes = NULL,
  organizationName = NULL,
  page = NULL,
  pathCategory = NULL,
  phenotypeId = NULL,
  pos = NULL,
  poss = NULL,
  project_id = NULL,
  .return_raw = NULL,
  rins = 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,
  .verbose = NULL
)

Value

A tibble of gtexr arguments and their metadata. Used for documentation only.

Arguments

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".
hardyScale: String A Hardy Scale of interest. Options: "Ventilator case", "Fast death - violent", "Fast death - natural causes", "Intermediate death", "Slow death".
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). Set globally to maximum value 100000 with options(list(gtexr.itemsPerPage = 100000)).
ischemicTimes: 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.
poss: Integer, vector.
project_id: String. Options: "gtex", "adult-gtex", "egtex".
.return_raw: Logical. If TRUE, return the raw API JSON response. Default = FALSE
rins: Integer, vector.
sampleId: String. ^GTEX-[A-Z0-9]{5}-[0-9]{4}-SM-[A-Z0-9]{5}$
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 get_tissue_site_detail() to see valid values) or an Ontology ID.
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.
uberonIds: Character vector of Uberon IDs (e.g. "UBERON:EFO_0000572"; use get_tissue_site_detail() to see valid values).
variantId: String. A gtex variant ID.
variantIds: Character vector. Gtex variant IDs.
.verbose: Logical. If TRUE (default), print paging information. Set to FALSE globally with options(list(gtexr.verbose = FALSE)).