gtexr
The goal of gtexr is to provide a convenient R interface to the GTEx Portal API V2.
The Genotype-Tissue Expression (GTEx) project is a comprehensive public resource for studying tissue-specific gene expression and regulation in human tissues. Through systematic analysis of RNA sequencing data from 54 non-diseased tissue sites across nearly 1000 individuals, GTEx provides crucial insights into the relationship between genetic variation and gene expression. This data is accessible through the GTEx Portal API, enabling programmatic access to human gene expression data.
New to R but want to explore the available data? Try out the interactive no-code ⭐shiny app⭐.
Installation
You can install this package from CRAN:
install.packages("gtexr")Or you can install the development version of gtexr from either GitHub with:
# install.packages("pak")
pak::pak("ropensci/gtexr") # source - GitHub… or R Universe with:
install.packages("gtexr", repos = "https://ropensci.r-universe.dev")Available functionality
- GTEx Portal API Info – Retrieve general service information about the GTEx API.
- Admin Endpoints – Access maintenance messages and news updates from GTEx.
- Static Association Endpoints – Query precomputed eQTL and sQTL associations across tissues.
- Dynamic Association Endpoints – Perform on-the-fly eQTL and sQTL calculations.
- Biobank Data Endpoints – Retrieve metadata on biobank samples.
- Datasets Endpoints – Access various GTEx dataset information, as well as variant annotation and linkage disequilibrium data.
- Expression Data Endpoints – Obtain expression levels across tissues, including gene, exon, junction, and transcript-level data.
- Histology Endpoints – Retrieve tissue histology image data.
- Reference Genome Endpoints – Query reference genome features, including genetic coordinates for genes, transcripts and exons, as well as reported phenotype associations for a region.
Examples
Get general information about the GTEx service:
library(gtexr)
get_service_info() |>
tibble::glimpse()
#> Rows: 1
#> Columns: 9
#> $ id <chr> "org.gtexportal.rest.v2"
#> $ name <chr> "GTEx Portal V2 API"
#> $ version <chr> "2.0.0"
#> $ organization_name <chr> "GTEx Project"
#> $ organization_url <chr> "https://gtexportal.org"
#> $ description <chr> "This service provides access to the data powering t…
#> $ contactUrl <chr> "https://gtexportal.org/home/contact"
#> $ documentationUrl <chr> "https://gtexportal.org/api/v2/docs"
#> $ environment <chr> "prod"Retrieve eQTL genes for whole blood tissue:[^1]
get_eqtl_genes("Whole_Blood")
#> Warning: ! Total number of items (12360) exceeds the selected maximum page size (250).
#> ✖ 12110 items were not retrieved.
#> ℹ To retrieve all available items, increase `itemsPerPage`, ensuring you reuse
#> your original query parameters e.g.
#> `get_eqtl_genes(<your_existing_parameters>, itemsPerPage = 100000)`
#> ℹ Alternatively, adjust global "gtexr.itemsPerPage" setting e.g.
#> `options(list(gtexr.itemsPerPage = 100000))`
#>
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 50
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 12360
#> # A tibble: 250 × 10
#> tissueSiteDetailId ontologyId datasetId empiricalPValue gencodeId geneSymbol
#> <chr> <chr> <chr> <dbl> <chr> <chr>
#> 1 Whole_Blood UBERON:001… gtex_v8 1.05e- 9 ENSG0000… WASH7P
#> 2 Whole_Blood UBERON:001… gtex_v8 1.06e-25 ENSG0000… RP11-34P1…
#> 3 Whole_Blood UBERON:001… gtex_v8 6.31e- 2 ENSG0000… CICP27
#> 4 Whole_Blood UBERON:001… gtex_v8 8.71e- 9 ENSG0000… RP11-34P1…
#> 5 Whole_Blood UBERON:001… gtex_v8 6.01e-20 ENSG0000… RP11-34P1…
#> 6 Whole_Blood UBERON:001… gtex_v8 6.96e- 9 ENSG0000… RP11-34P1…
#> 7 Whole_Blood UBERON:001… gtex_v8 3.10e- 4 ENSG0000… RP11-34P1…
#> 8 Whole_Blood UBERON:001… gtex_v8 1.92e- 3 ENSG0000… ABC7-4304…
#> 9 Whole_Blood UBERON:001… gtex_v8 1.58e- 3 ENSG0000… RP11-34P1…
#> 10 Whole_Blood UBERON:001… gtex_v8 7.82e- 2 ENSG0000… AP006222.2
#> # ℹ 240 more rows
#> # ℹ 4 more variables: log2AllelicFoldChange <dbl>, pValue <dbl>,
#> # pValueThreshold <dbl>, qValue <dbl>Retrieve significant eQTLs for one or more genes:
get_significant_single_tissue_eqtls(gencodeId = c(
"ENSG00000132693.12",
"ENSG00000203782.5"
))
#>
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 249
#> # A tibble: 249 × 13
#> snpId pos snpIdUpper variantId geneSymbol pValue geneSymbolUpper
#> <chr> <int> <chr> <chr> <chr> <dbl> <chr>
#> 1 rs12128960 159343657 RS12128960 chr1_1593… CRP 8.52e-5 CRP
#> 2 rs12132451 159344052 RS12132451 chr1_1593… CRP 7.92e-5 CRP
#> 3 rs12136402 159347493 RS12136402 chr1_1593… CRP 7.92e-5 CRP
#> 4 rs10908709 159350390 RS10908709 chr1_1593… CRP 7.92e-5 CRP
#> 5 rs10908710 159351189 RS10908710 chr1_1593… CRP 7.92e-5 CRP
#> 6 rs11265178 159359256 RS11265178 chr1_1593… CRP 9.62e-5 CRP
#> 7 rs35532309 159360755 RS35532309 chr1_1593… CRP 6.11e-5 CRP
#> 8 rs6692378 159369451 RS6692378 chr1_1593… CRP 1.17e-6 CRP
#> 9 rs10908714 159370563 RS10908714 chr1_1593… CRP 1.80e-5 CRP
#> 10 rs6656924 159372915 RS6656924 chr1_1593… CRP 1.00e-6 CRP
#> # ℹ 239 more rows
#> # ℹ 6 more variables: datasetId <chr>, tissueSiteDetailId <chr>,
#> # ontologyId <chr>, chromosome <chr>, gencodeId <chr>, nes <dbl>Citing gtexr
If you find gtexr useful, please consider citing both GTEx and gtexr. Citation details are available here.
Example publications citing gtexr include:
Community guidelines
Feedback, bug reports, and feature requests are welcome; file issues or seek support here. If you would like to contribute to the package, please see our contributing guidelines.
Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
[^1]: Note the warning raised if the number of items returned by a
function call exceeds the requested page size. Argument
itemsPerPage is set to 250 by default, but may be increased to
ensure that all items are retrieved in one go.