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Get Genes

Source: R/get_genes.R
get_genes.Rd

This service returns information about reference genes. A genome build and GENCODE version must be provided.

  • Genes are searchable by gene symbol, GENCODE ID and versioned GENCODE ID.

  • Versioned GENCODE ID is recommended to ensure unique ID matching.

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

GTEx API Portal documentation

Usage

get_genes(
  geneIds,
  gencodeVersion = "v26",
  genomeBuild = "GRCh38/hg38",
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Arguments

geneIds

A character vector of gene symbols, versioned gencodeIds, or unversioned gencodeIds.

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_genomic_features(), get_gwas_catalog_by_location(), get_neighbor_gene(), get_transcripts()

Examples

get_genes(c("CRP", "IL6R"))
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 2
#> # A tibble: 2 × 15
#>   chromosome dataSource description    end entrezGeneId gencodeId gencodeVersion
#>   <chr>      <chr>      <chr>        <int>        <int> <chr>     <chr>         
#> 1 chr1       HAVANA     interleuki… 1.54e8         3570 ENSG0000… v26           
#> 2 chr1       HAVANA     C-reactive… 1.60e8         1401 ENSG0000… v26           
#> # ℹ 8 more variables: geneStatus <chr>, geneSymbol <chr>,
#> #   geneSymbolUpper <chr>, geneType <chr>, genomeBuild <chr>, start <int>,
#> #   strand <chr>, tss <int>