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Get Eqtl Genes

Source: R/get_eqtl_genes.R
get_eqtl_genes.Rd

Retrieve eGenes (eQTL Genes).

  • This service returns eGenes (eQTL Genes) from the specified dataset.

  • eGenes are genes that have at least one significant cis-eQTL acting upon them.

  • Results may be filtered by tissue. By default, the service queries the latest GTEx release.

For each eGene, the results include the allelic fold change (log2AllelicFoldChange), p-value (pValue), p-value threshold (pValueThreshold), empirical p-value (empiricalPValue), and q-value (qValue).

  • The log2AllelicFoldChange is the allelic fold change (in log2 scale) of the most significant eQTL.

  • The pValue is the nominal p-value of the most significant eQTL.

  • The pValueThreshold is the p-value threshold used to determine whether a cis-eQTL for this gene is significant. For more details see https://gtexportal.org/home/documentationPage#staticTextAnalysisMethods.

  • The empiricalPValue is the beta distribution-adjusted empirical p-value from FastQTL.

  • The qValues were calculated based on the empirical p-values. A false discovery rate (FDR) threshold of <= 0.05 was applied to identify genes with a significant eQTL.

GTEx Portal API documentation.

Usage

get_eqtl_genes(
  tissueSiteDetailIds,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = 250
)

Arguments

tissueSiteDetailIds

Character vector of IDs for tissues of interest. Can be GTEx specific IDs (e.g. "Whole_Blood"; use get_tissue_site_detail() to see valid values) or Ontology IDs.

datasetId

String. Unique identifier of a dataset. Usually includes a data source and data release. Options: "gtex_v8", "gtex_snrnaseq_pilot".

page

Integer (default = 0).

itemsPerPage

Integer (default = 250).

Value

A tibble.

See also

Other Static Association Endpoints: get_fine_mapping(), get_independent_eqtl(), get_multi_tissue_eqtls(), get_significant_single_tissue_eqtls(), get_significant_single_tissue_eqtls_by_location(), get_significant_single_tissue_ieqtls(), get_significant_single_tissue_isqtls(), get_significant_single_tissue_sqtls(), get_sqtl_genes()

Examples

if (FALSE) { # \dontrun{
get_eqtl_genes(c("Whole_Blood", "Artery_Aorta"))
} # }