gtexr (version 0.2.1)

get_eqtl_genes: Get Eqtl Genes

Description

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 = NULL,
  datasetId = "gtex_v8",
  page = 0,
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Value

A tibble. Or a list if .return_raw = TRUE.

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). Set globally to maximum value 100000 with options(list(gtexr.itemsPerPage = 100000)).

.verbose

Logical. If TRUE (default), print paging information. Set to FALSE globally with options(list(gtexr.verbose = FALSE)).

.return_raw

Logical. If TRUE, return the raw API JSON response. Default = FALSE

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) { # identical(Sys.getenv("IN_PKGDOWN"), "true")
get_eqtl_genes(c("Whole_Blood", "Artery_Aorta"))
}