Get eQTL details by gene ensembl identifier

This function retrieves eQTLs, along with its genomic position, beta values and p-values.

get_eqtl_pval_by_gene(
  ensembl_id,
  species_name = "homo_sapiens",
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

Arguments

ensembl_id	An Ensembl stable identifier, e.g. "ENSG00000248234378" (or a vector thereof).
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 10 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'.

ensembl_id

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

variant_id

Variant identifier, e.g. "rs80100814".

tissue

Tissue.

display_consequence

Variant consequence type.

seq_region_name

Sequence region name (typically a chromosome name) of the variant.

seq_region_start

Genomic start position of the variant.

seq_region_end

Genomic end position of the variant.

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_gene() makes GET requests to /eqtl/id/:species/:stable_id.

Examples

get_eqtl_pval_by_gene('ENSG00000248378')
#> # A tibble: 0 × 10
#> # … with 10 variables: species_name <chr>, ensembl_id <chr>, variant_id <chr>,
#> #   tissue <chr>, display_consequence <chr>, seq_region_name <chr>,
#> #   seq_region_start <int>, seq_region_end <int>, beta <dbl>, pvalue <dbl>