This page documents functions using the IGVF 'REST' API, documented at https://api.catalog.igvf.org/#
gene_variants() locates GTEx eQTLs and splice QTLs
associate with a gene using the IGVF 'catalog' API. Only one of
gene_id, hgnc, gene_name, or alias should be specified.
Usage
gene_variants(
gene_id = NULL,
hgnc = NULL,
gene_name = NULL,
alias = NULL,
organism = "Homo sapiens",
verbose = FALSE
)Arguments
- gene_id
character(1) Ensembl gene identifier, e.g., "ENSG00000106633"
- hgnc
character(1) HGNC identifier.
- gene_name
character(1) Gene symbol, e.g., "GCK"
- alias
character(1) Gene alias
- organism
character(1) Either 'Homo sapiens' (default) or 'Mus musculus'.
- verbose
logical(1) return additional information about variants and genes.
Value
gene_variants() returns a tibble describing variants
associated with the gene; use verbose = TRUE to retrieve more
extensive information.
Examples
gene_variants(gene_name = "GCK")
#> # A tibble: 25 × 9
#> `sequence variant` gene label log10pvalue effect_size source source_url
#> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr>
#> 1 variants/8c6a683829bcb… gene… eQTL 4.89 0.274 GTEx https://s…
#> 2 variants/cf796b5a16212… gene… eQTL 5.76 0.221 GTEx https://s…
#> 3 variants/9a36af4633321… gene… eQTL 6.17 -0.266 GTEx https://s…
#> 4 variants/2fefe07a0750b… gene… eQTL 3.69 0.158 GTEx https://s…
#> 5 variants/ab6df1152a643… gene… eQTL 16.9 -0.353 GTEx https://s…
#> 6 variants/92833b52621e5… gene… eQTL 4.86 -0.170 GTEx https://s…
#> 7 variants/bceca4e6ac3cd… gene… eQTL 4.63 -0.340 GTEx https://s…
#> 8 variants/0a8ba63e5451a… gene… eQTL 4.94 0.215 GTEx https://s…
#> 9 variants/80f639e0da643… gene… eQTL 6.59 -0.330 GTEx https://s…
#> 10 variants/7f4ca6f1cfd70… gene… eQTL 4.10 -0.165 GTEx https://s…
#> # ℹ 15 more rows
#> # ℹ 2 more variables: biological_context <chr>, chr <chr>
response <- gene_variants(gene_name = "GCK", verbose = TRUE)
response
#> # A tibble: 25 × 9
#> `sequence variant` gene label log10pvalue effect_size source
#> <list> <list> <chr> <dbl> <dbl> <chr>
#> 1 <named list [14]> <named list [11]> eQTL 4.89 0.274 GTEx
#> 2 <named list [14]> <named list [11]> eQTL 5.76 0.221 GTEx
#> 3 <named list [14]> <named list [11]> eQTL 6.17 -0.266 GTEx
#> 4 <named list [14]> <named list [11]> eQTL 3.69 0.158 GTEx
#> 5 <named list [14]> <named list [11]> eQTL 16.9 -0.353 GTEx
#> 6 <named list [14]> <named list [11]> eQTL 4.86 -0.170 GTEx
#> 7 <named list [14]> <named list [11]> eQTL 4.63 -0.340 GTEx
#> 8 <named list [14]> <named list [11]> eQTL 4.94 0.215 GTEx
#> 9 <named list [14]> <named list [11]> eQTL 6.59 -0.330 GTEx
#> 10 <named list [14]> <named list [11]> eQTL 4.10 -0.165 GTEx
#> # ℹ 15 more rows
#> # ℹ 3 more variables: source_url <chr>, biological_context <chr>, chr <chr>
response |>
dplyr::select(`sequence variant`) |>
tidyr::unnest_wider(`sequence variant`)
#> # A tibble: 25 × 14
#> organism `_id` chr pos rsid ref alt spdi hgvs qual filter
#> <chr> <chr> <chr> <int> <chr> <chr> <chr> <chr> <chr> <chr> <lgl>
#> 1 Homo sapiens 8c6a683… chr7 4.41e7 rs25… G A NC_0… NC_0… . NA
#> 2 Homo sapiens cf796b5… chr7 4.41e7 rs29… T C NC_0… NC_0… . NA
#> 3 Homo sapiens 9a36af4… chr7 4.41e7 rs11… GT G NC_0… NC_0… . NA
#> 4 Homo sapiens 2fefe07… chr7 4.43e7 rs28… G A NC_0… NC_0… . NA
#> 5 Homo sapiens ab6df11… chr7 4.41e7 rs22… C G NC_0… NC_0… . NA
#> 6 Homo sapiens 92833b5… chr7 4.41e7 rs41… G A NC_0… NC_0… . NA
#> 7 Homo sapiens bceca4e… chr7 4.40e7 rs76… T G NC_0… NC_0… . NA
#> 8 Homo sapiens 0a8ba63… chr7 4.41e7 rs25… A G NC_0… NC_0… . NA
#> 9 Homo sapiens 80f639e… chr7 4.41e7 rs14… A AG NC_0… NC_0… . NA
#> 10 Homo sapiens 7f4ca6f… chr7 4.42e7 rs29… A T NC_0… NC_0… . NA
#> # ℹ 15 more rows
#> # ℹ 3 more variables: annotations <list>, source <chr>, source_url <chr>