View source: R/get_eqtl_genes.R
get_eqtl_genes | R Documentation |
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.
get_eqtl_genes(
tissueSiteDetailIds,
datasetId = "gtex_v8",
page = 0,
itemsPerPage = 250
)
tissueSiteDetailIds |
Character vector of IDs for tissues of interest.
Can be GTEx specific IDs (e.g. "Whole_Blood"; use
|
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). |
A tibble.
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()
## Not run:
get_eqtl_genes(c("Whole_Blood", "Artery_Aorta"))
## End(Not run)
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