otargen (version 2.0.0)

gwasColocalisation: Retrieve calculated GWAS colocalisation data

Description

This function retrieves colocalisation data for a specific study locus from a GWAS study with other GWAS studies. It returns a data frame of the studies that colocalise with the input study locus, including details on the study, reported trait, index variant, and calculated colocalisation method outputs.

Usage

gwasColocalisation(study_locus_id, size = 500, index = 0)

Value

Returns a data frame of the studies that colocalise with the input study locus. The table consists of the following data structure:

• study.studyId: Character vector. Study identifier.

• study.traitReported: Character vector. Reported trait associated with the colocalisation.

• study.projectId: Character vector. Project identifier for the study.

• study.publicationFirstAuthor: Character vector. First author of the publication.

• indexVariant.id: Character vector. Index variant identifier.

• indexVariant.position: Integer vector. Index variant position.

• indexVariant.chromosome: Character vector. Index variant chromosome.

• indexVariant.referenceAllele: Character vector. Reference allele of the variant.

• indexVariant.alternateAllele: Character vector. Alternate allele of the variant.

• pValueMantissa: Numeric vector. Mantissa of the p-value for the colocalisation.

• pValueExponent: Integer vector. Exponent of the p-value for the colocalisation.

• numberColocalisingVariants: Integer vector. Number of colocalising variants.

• colocalisationMethod: Character vector. Method used for colocalisation analysis.

• h3: Numeric vector. H3 value associated with the colocalisation.

• h4: Numeric vector. H4 value associated with the colocalisation.

• clpp: Numeric vector. Colocalisation posterior probability.

• betaRatioSignAverage: Numeric vector. Average sign of the beta ratio.

Arguments

study_locus_id

Character: Open Target Genetics generated ID for the study locus (e.g., "5a86bfd40d2ebecf6ce97bbe8a737512").

size

Integer: Number of rows to fetch per page. Default: 500.

index

Integer: Page index for pagination. Default: 0.

References

Giambartolomei, Claudia et al. “Bayesian test for colocalisation between pairs of genetic association studies using summary statistics.” PLoS genetics vol. 10,5 e1004383. 15 May. 2014, doi:10.1371/journal.pgen.1004383

Examples

if (FALSE) {
colocalisation_data <- gwasColocalisation(study_locus_id = "5a86bfd40d2ebecf6ce97bbe8a737512",
 size = 500, index = 0)
}