Get eQTL details by variant identifier

This function retrieves genes (Ensembl identifier) along with beta values and p-values for the eQTL association.

get_eqtl_pval_by_variant(
  variant_id,
  species_name = "homo_sapiens",
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

Arguments

variant_id	A variant identifier, e.g. "rs80100814".
species_name	The species name, i.e., the scientific name, all letters lowercase and space replaced by underscore. Currently, only 'homo_sapiens' (human) is supported.
verbose	Whether to be verbose about the http requests and respective responses' status.
warnings	Whether to show warnings.
progress_bar	Whether to show a progress bar.

Value

A tibble of 6 variables:

species_name

Ensembl species name: this is the name used internally by Ensembl to uniquely identify a species by name. It is the scientific name but formatted without capitalisation and spacing converted with an underscore, e.g., 'homo_sapiens'.

variant_id

Variant identifier, e.g. "rs80100814".

ensembl_id

An Ensembl stable identifier, e.g. "ENSG00000248234378".

tissue

Tissue.

beta

The effect size beta of the eQTL association analysis.

pvalue

The p-value of the eQTL association analysis.

Ensembl REST API endpoints

get_eqtl_pval_by_variant() makes GET requests to /eqtl/variant_name/:species/:variant_name.

Examples

get_eqtl_pval_by_variant('rs80100814')
#> # A tibble: 452 × 6
#>    species_name variant_id ensembl_id      tissue                   beta pvalue
#>    <chr>        <chr>      <chr>           <chr>                   <dbl>  <dbl>
#>  1 homo_sapiens rs80100814 ENSG00000136237 Adipose_Subcutaneous -0.00990 0.953 
#>  2 homo_sapiens rs80100814 ENSG00000233476 Adipose_Subcutaneous -0.0271  0.835 
#>  3 homo_sapiens rs80100814 ENSG00000232759 Adipose_Subcutaneous -0.331   0.0776
#>  4 homo_sapiens rs80100814 ENSG00000232949 Adipose_Subcutaneous  0.100   0.647 
#>  5 homo_sapiens rs80100814 ENSG00000105889 Adipose_Subcutaneous  0.0281  0.893 
#>  6 homo_sapiens rs80100814 ENSG00000136244 Adipose_Subcutaneous  0.0885  0.551 
#>  7 homo_sapiens rs80100814 ENSG00000179428 Adipose_Subcutaneous -0.261   0.204 
#>  8 homo_sapiens rs80100814 ENSG00000196683 Adipose_Subcutaneous -0.173   0.163 
#>  9 homo_sapiens rs80100814 ENSG00000228649 Adipose_Subcutaneous  0.0905  0.644 
#> 10 homo_sapiens rs80100814 ENSG00000226329 Adipose_Subcutaneous  0.0103  0.957 
#> # … with 442 more rows