gtexr (version 0.2.1)

get_exons: Get Exons

Description

This service returns exons from all known transcripts of the given gene.

• A versioned GENCODE ID is required to ensure that all exons are from a single gene.

• A dataset ID or both GENCODE version and genome build must be provided.

• Although annotated exons are not dataset dependent, specifying a dataset here is equivalent to specifying the GENCODE version and genome build used by that dataset.

GTEx Portal API documentation

Usage

get_exons(
  gencodeIds,
  gencodeVersion = NULL,
  genomeBuild = NULL,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Value

A tibble. Or a list if .return_raw = TRUE.

Arguments

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".

genomeBuild

String. Options: "GRCh38/hg38", "GRCh37/hg19". Default = "GRCh38/hg38".

datasetId

String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot".

page

Integer (default = 0).

itemsPerPage

Integer (default = 250). Set globally to maximum value 100000 with options(list(gtexr.itemsPerPage = 100000)).

.verbose

Logical. If TRUE (default), print paging information. Set to FALSE globally with options(list(gtexr.verbose = FALSE)).

.return_raw

Logical. If TRUE, return the raw API JSON response. Default = FALSE

See Also

Other Reference Genome Endpoints: get_gene_search(), get_genes(), get_genomic_features(), get_gwas_catalog_by_location(), get_neighbor_gene(), get_transcripts()

Examples

if (FALSE) { # identical(Sys.getenv("IN_PKGDOWN"), "true")
get_exons(gencodeIds = c("ENSG00000132693.12", "ENSG00000203782.5"))
}