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Get Top Expressed Genes

Source: R/get_top_expressed_genes.R
get_top_expressed_genes.Rd

Find top expressed genes for a specified tissue.

  • Returns top expressed genes for a specified tissue in a dataset, sorted by median expression.

  • When the optional parameter filterMtGene is set to true, mitochondrial genes will be excluded from the results. By default, this service queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_top_expressed_genes(
  tissueSiteDetailId,
  datasetId = "gtex_v8",
  filterMtGene = TRUE,
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Arguments

tissueSiteDetailId

String. The ID of the tissue of interest. Can be a GTEx specific ID (e.g. "Whole_Blood"; use get_tissue_site_detail() to see valid values) or an Ontology ID.

datasetId

String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot".

filterMtGene

Logical. Exclude mitochondrial genes.

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 Expression Data Endpoints: get_clustered_median_exon_expression(), get_clustered_median_gene_expression(), get_clustered_median_junction_expression(), get_clustered_median_transcript_expression(), get_expression_pca(), get_gene_expression(), get_median_exon_expression(), get_median_gene_expression(), get_median_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary()

Examples

get_top_expressed_genes(tissueSiteDetailId = "Artery_Aorta")
#> Warning: ! Total number of items (56163) exceeds the selected maximum page size (250).
#> ✖ 55913 items were not retrieved.
#> ℹ To retrieve all available items, increase `itemsPerPage`, ensuring you reuse
#>   your original query parameters e.g.
#>   `get_top_expressed_genes(<your_existing_parameters>, itemsPerPage = 100000)`
#> ℹ Alternatively, adjust global "gtexr.itemsPerPage" setting e.g.
#>   `options(list(gtexr.itemsPerPage = 100000))`
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 225
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 56163
#> # A tibble: 250 × 7
#>    tissueSiteDetailId ontologyId     datasetId gencodeId geneSymbol median unit 
#>    <chr>              <chr>          <chr>     <chr>     <chr>       <dbl> <chr>
#>  1 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… MGP        11936. TPM  
#>  2 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… FTL         9196. TPM  
#>  3 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… ACTB        9154. TPM  
#>  4 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… BGN         8167. TPM  
#>  5 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… TAGLN       6099. TPM  
#>  6 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… ACTA2       5736. TPM  
#>  7 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… IGFBP7      5639. TPM  
#>  8 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… MYL9        4275. TPM  
#>  9 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… HSPB1       3780. TPM  
#> 10 Artery_Aorta       UBERON:0001496 gtex_v8   ENSG0000… FLNA        3732. TPM  
#> # ℹ 240 more rows