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Get Transcripts

Source: R/get_transcripts.R
get_transcripts.Rd

Find all transcripts of a reference gene.

  • This service returns information about transcripts of the given versioned GENCODE ID.

  • A genome build and GENCODE version must be provided.

  • By default, this service queries the genome build and GENCODE version used by the latest GTEx release.

GTEx API Portal documentation

Usage

get_transcripts(
  gencodeId,
  gencodeVersion = "v26",
  genomeBuild = "GRCh38/hg38",
  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".

gencodeVersion

String (default = "v26"). GENCODE annotation release. Either "v26" or "v19".

genomeBuild

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

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_exons(), get_gene_search(), get_genes(), get_genomic_features(), get_gwas_catalog_by_location(), get_neighbor_gene()

Examples

get_transcripts(gencodeId = "ENSG00000203782.5")
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 1
#> # A tibble: 1 × 11
#>    start    end featureType genomeBuild transcriptId source chromosome gencodeId
#>    <int>  <int> <chr>       <chr>       <chr>        <chr>  <chr>      <chr>    
#> 1 1.53e8 1.53e8 transcript  GRCh38/hg38 ENST0000036… HAVANA chr1       ENSG0000…
#> # ℹ 3 more variables: geneSymbol <chr>, gencodeVersion <chr>, strand <chr>