Get Median Gene Expression

Find median gene expression data along with hierarchical clusters.

• Returns median gene expression in tissues.

• By default, this endpoint queries the latest GTEx release.

GTEx Portal API documentation

Usage

get_median_gene_expression(
  gencodeIds,
  datasetId = "gtex_v8",
  tissueSiteDetailIds = NULL,
  page = 0,
  itemsPerPage = 250
)

Arguments

gencodeIds

A character vector of Versioned GENCODE IDs, e.g. c("ENSG00000132693.12", "ENSG00000203782.5").

datasetId

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

tissueSiteDetailIds

Character vector of IDs for tissues of interest. Can be GTEx specific IDs (e.g. "Whole_Blood"; use get_tissue_site_detail() to see valid values) or Ontology IDs.

page

Integer (default = 0).

itemsPerPage

Integer (default = 250).

Value

A tibble.

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_junction_expression(), get_median_transcript_expression(), get_single_nucleus_gex(), get_single_nucleus_gex_summary(), get_top_expressed_genes()

Examples

# \dontrun{
get_median_gene_expression(gencodeIds = "ENSG00000132693.12")
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 54
#> # A tibble: 54 × 7
#>    median tissueSiteDetailId     ontologyId datasetId gencodeId geneSymbol unit 
#>     <dbl> <chr>                  <chr>      <chr>     <chr>     <chr>      <chr>
#>  1 0.347  Adipose_Subcutaneous   UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#>  2 0.240  Adipose_Visceral_Omen… UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#>  3 0.384  Adrenal_Gland          UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#>  4 0.198  Artery_Aorta           UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#>  5 0.332  Artery_Coronary        UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#>  6 0.117  Artery_Tibial          UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#>  7 0.631  Bladder                UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#>  8 0.0347 Brain_Amygdala         UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#>  9 0.0433 Brain_Anterior_cingul… UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#> 10 0.0226 Brain_Caudate_basal_g… UBERON:00… gtex_v8   ENSG0000… CRP        TPM  
#> # ℹ 44 more rows
# }