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Get Gene Search

Source: R/get_gene_search.R
get_gene_search.Rd

Find genes that are partial or complete match of a gene_id

  • gene_id could be a gene symbol, a gencode ID, or an Ensemble ID

  • Gencode Version and Genome Build must be specified

GTEx Portal API documentation

Usage

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

Arguments

geneId

String. A gene symbol, a gencode ID, or an Ensemble ID.

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_genes(), get_genomic_features(), get_gwas_catalog_by_location(), get_neighbor_gene(), get_transcripts()

Examples

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