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Get Exons

Source: R/get_exons.R
get_exons.Rd

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
)

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

Value

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

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

get_exons(gencodeIds = c("ENSG00000132693.12", "ENSG00000203782.5"))
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 23
#> # A tibble: 23 × 13
#>    featureType       end genomeBuild    start exonId source chromosome gencodeId
#>    <chr>           <int> <chr>          <int> <chr>  <chr>  <chr>      <chr>    
#>  1 exon        153259733 GRCh38/hg38   1.53e8 ENSE0… HAVANA chr1       ENSG0000…
#>  2 exon        153262122 GRCh38/hg38   1.53e8 ENSE0… HAVANA chr1       ENSG0000…
#>  3 exon        159714589 GRCh38/hg38   1.60e8 ENSE0… HAVANA chr1       ENSG0000…
#>  4 exon        159714138 GRCh38/hg38   1.60e8 ENSE0… HAVANA chr1       ENSG0000…
#>  5 exon        159713767 GRCh38/hg38   1.60e8 ENSE0… HAVANA chr1       ENSG0000…
#>  6 exon        159712794 GRCh38/hg38   1.60e8 ENSE0… HAVANA chr1       ENSG0000…
#>  7 exon        159714589 GRCh38/hg38   1.60e8 ENSE0… ENSEM… chr1       ENSG0000…
#>  8 exon        159713972 GRCh38/hg38   1.60e8 ENSE0… ENSEM… chr1       ENSG0000…
#>  9 exon        159712794 GRCh38/hg38   1.60e8 ENSE0… ENSEM… chr1       ENSG0000…
#> 10 exon        159714589 GRCh38/hg38   1.60e8 ENSE0… HAVANA chr1       ENSG0000…
#> # ℹ 13 more rows
#> # ℹ 5 more variables: transcriptId <chr>, geneSymbol <chr>,
#> #   gencodeVersion <chr>, strand <chr>, exonNumber <chr>