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gtexr arguments

Source: R/gtexr_arguments.R
gtexr_arguments.Rd

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
)

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)).

Value

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