Median expression across tissues — gtex_median

Two requests: one to resolve the versioned GENCODE id, one for the expression. See gtex_gene_reference() for why the first is unavoidable.

Usage

gtex_median_expression(
  gene = NULL,
  gencode_id = NULL,
  dataset = GTEX_DATASET,
  ...
)

Arguments

gene: A gene symbol or an Ensembl gene id. Ignored when gencode_id is given.
gencode_id: A versioned GENCODE id, for example "ENSG00000141510.16".
dataset: The GTEx dataset. Must match the reference the id came from.
...: Passed to biohttp::get_json(), for example throttle.

Value

A biohttp envelope whose data is the tibble described in gtex_parse_expression().

Details

Pass gencode_id directly to skip the lookup when you already have a versioned id.

References

The GTEx Consortium (2020). The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369(6509), 1318-1330. doi:10.1126/science.aaz1776

Service documentation: https://gtexportal.org/home/

Examples

# \donttest{
biohttp::body_or_null(gtex_median_expression("TP53"))
#> # A tibble: 54 × 4
#>    tissue_id                            tissue             median_tpm gencode_id
#>    <chr>                                <chr>                   <dbl> <chr>     
#>  1 Adipose_Subcutaneous                 Adipose Subcutane…      22.5  ENSG00000…
#>  2 Adipose_Visceral_Omentum             Adipose Visceral …      17.8  ENSG00000…
#>  3 Adrenal_Gland                        Adrenal Gland           13.5  ENSG00000…
#>  4 Artery_Aorta                         Artery Aorta            18.5  ENSG00000…
#>  5 Artery_Coronary                      Artery Coronary         19.7  ENSG00000…
#>  6 Artery_Tibial                        Artery Tibial           20.5  ENSG00000…
#>  7 Bladder                              Bladder                 23.8  ENSG00000…
#>  8 Brain_Amygdala                       Brain Amygdala           3.66 ENSG00000…
#>  9 Brain_Anterior_cingulate_cortex_BA24 Brain Anterior ci…       3.13 ENSG00000…
#> 10 Brain_Caudate_basal_ganglia          Brain Caudate bas…       4.02 ENSG00000…
#> # ℹ 44 more rows
# }