Get Collapsed Gene Model Exon

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

get_collapsed_gene_model_exon(gencodeId = "ENSG00000132693.12")
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 2
#> # A tibble: 2 × 14
#>   featureType       end genomeBuild chromosome exonNumber geneSymbolUpper exonId
#>   <chr>           <int> <chr>       <chr>      <chr>      <chr>           <chr> 
#> 1 exon        159714589 GRCh38/hg38 chr1       1          CRP             ENSG0…
#> 2 exon        159714138 GRCh38/hg38 chr1       2          CRP             ENSG0…
#> # ℹ 7 more variables: datasetId <chr>, start <int>, dataSource <chr>,
#> #   gencodeId <chr>, geneSymbol <chr>, gencodeVersion <chr>, strand <chr>