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Retrieve calculated GWAS colocalisation data

Source: R/GWASColocQuery.R
gwasColocalisation.Rd

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)

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.

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.

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) { # \dontrun{
colocalisation_data <- gwasColocalisation(study_locus_id = "5a86bfd40d2ebecf6ce97bbe8a737512",
 size = 500, index = 0)
} # }