get_collapsed_gene_model_exon: Get Collapsed Gene Model Exon

In gtexr: Query the GTEx Portal API

Get Collapsed Gene Model Exon

Description

This service returns the collapsed exons in the gene model of the given gene. Gene-level and exon-level expression quantification were based on the GENCODE annotation, collapsed to a single transcript model for each gene using an algorithm developed by the GTEx analysis team.

By default, this service queries the models used by the latest GTEx release.

GTEx Portal API documentation

Usage

get_collapsed_gene_model_exon(
  gencodeId,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Arguments

gencodeId	String. A Versioned GENCODE ID of a gene, e.g. "ENSG00000065613.9".
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

Value

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

See Also

Other Datasets Endpoints: get_annotation(), get_downloads_page_data(), get_file_list(), get_full_get_collapsed_gene_model_exon(), get_functional_annotation(), get_linkage_disequilibrium_by_variant_data(), get_linkage_disequilibrium_data(), get_sample_datasets(), get_subject(), get_tissue_site_detail(), get_variant(), get_variant_by_location()

Examples

## Not run: 
get_collapsed_gene_model_exon(gencodeId = "ENSG00000132693.12")

## End(Not run)

gtexr documentation built on June 8, 2025, 10:26 a.m.