Turn a GTEx median-expression response into a table — gtex_parse

Pure. Tissue ids arrive underscore-separated (Adipose_Subcutaneous) and are returned both raw and as a readable label.

Usage

gtex_parse_expression(body)

Arguments

body: A parsed GTEx expression/medianGeneExpression response.

Value

A tibble of tissue_id, tissue, median_tpm, and gencode_id. Rows with no median are dropped. NULL when there is nothing usable.

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

body <- list(data = list(list(
  median = 22.459, tissueSiteDetailId = "Adipose_Subcutaneous",
  gencodeId = "ENSG00000141510.16", unit = "TPM"
)))
gtex_parse_expression(body)
#> # A tibble: 1 × 4
#>   tissue_id            tissue               median_tpm gencode_id        
#>   <chr>                <chr>                     <dbl> <chr>             
#> 1 Adipose_Subcutaneous Adipose Subcutaneous       22.5 ENSG00000141510.16