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Retrieve PheWAS (Phenome Wide Association Studies) data for a variant.

Source: R/pheWAS.R
pheWAS.Rd

PheWAS (Phenome-wide association study) is a method that investigates the relationships between genetic variants and traits or phenotypes, helping in the study of their potential influence on multiple traits or diseases concurrently. This function retrieves the traits associated with a given variant in the UK Biobank, FinnGen, and/or GWAS Catalog summary statistics repository (only traits with a p-value less than 0.005 are returned).

Usage

pheWAS(variant_id)

Arguments

variant_id

Character: generated ID for variants by Open Targets Genetics (e.g. 1_154119580_C_A) or rsId (rs2494663).

Value

A data frame with PheWAS associations.

The output data frame contains the following columns:

  • totalGWASStudies: An integer indicating the total number of GWAS studies where the variant is associated.

  • pval: A numeric value representing the p-value of the association between the variant and the trait.

  • beta: A numeric value representing the beta value, which represents the effect size of the variant on the trait.

  • oddsRatio: A numeric value representing the odds ratio, measuring the association between the variant and the trait.

  • nTotal: An integer indicating the total number of participants in the study.

  • study.studyId: A character vector representing the study ID.

  • study.source: A character vector representing the source of the study.

  • study.pmid: A character vector representing the PubMed ID (PMID) of the study.

  • study.pubDate: A character vector representing the publication date of the study.

  • study.traitReported: A character vector representing the reported trait associated with the variant.

  • study.traitCategory: A character vector representing the category of the trait.

References

Pendergrass, S A et al. “The use of phenome-wide association studies (PheWAS) for exploration of novel genotype-phenotype relationships and pleiotropy discovery.” Genetic epidemiology vol. 35,5 (2011): 410-22. doi:10.1002/gepi.20589

Examples

if (FALSE) {
result <- pheWAS(variant_id = "1_154549918_C_A")
result <- pheWAS(variant_id = "rs72698179")
}