gwasColocalisation {otargen} | R Documentation |
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)
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
## Not run:
colocalisation_data <- gwasColocalisation(study_locus_id = "5a86bfd40d2ebecf6ce97bbe8a737512",
size = 500, index = 0)
## End(Not run)