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Retrieves tag variants and studies for a given index variant.

Source: R/tagVariantsAndStudiesForIndexVariant.R
tagVariantsAndStudiesForIndexVariant.Rd

For an input index variant ID, this function fetches information about the tag variants and associated studies, including scores.

Usage

tagVariantsAndStudiesForIndexVariant(variant_id, pageindex = 0, pagesize = 20)

Arguments

variant_id

Character: Open Targets Genetics generated ID for a variant (CHRPOSITION_REFALLELE_ALTALLELE or rsId).

pageindex

Integer: Index of the current page for pagination (>= 0).

pagesize

Integer: Number of records in a page for pagination (> 0).

Value

Returns a data frame containing the variant associations connected to the input index variant. The columns in the data frame are as follows:

  • tagVariant.id: Character. Tag variant ID.

  • tagVariant.chromosome: Character. Chromosome of the tag variant.

  • tagVariant.rsId: Character. rsID of the tag variant.

  • tagVariant.position: Integer. Position of the tag variant.

  • study.studyId: Character. Study ID.

  • study.traitReported: Character. Reported trait of the study.

  • study.traitCategory: Character. Category of the trait in the study.

  • pval: Numeric. P-value.

  • pvalMantissa: Numeric. Mantissa of the p-value.

  • pvalExponent: Integer. Exponent of the p-value.

  • nTotal: Integer. Total number of samples.

  • nCases: Integer. Number of cases in the study.

  • overallR2: Numeric. Overall R-squared value.

  • afr1000GProp: Numeric. Proportion in African 1000 Genomes population.

  • amr1000GProp: Numeric. Proportion in Admixed American 1000 Genomes population.

  • eas1000GProp: Numeric. Proportion in East Asian 1000 Genomes population.

  • eur1000GProp: Numeric. Proportion in European 1000 Genomes population.

  • sas1000GProp: Numeric. Proportion in South Asian 1000 Genomes population.

  • oddsRatio: Numeric. Odds ratio.

  • oddsRatioCILower: Numeric. Lower bound of the odds ratio confidence interval.

  • oddsRatioCIUpper: Numeric. Upper bound of the odds ratio confidence interval.

  • posteriorProbability: Numeric. Posterior probability.

  • beta: Numeric. Beta value.

  • betaCILower: Numeric. Lower bound of the beta value confidence interval.

  • betaCIUpper: Numeric. Upper bound of the beta value confidence interval.

  • direction: Character. Direction of the effect.

  • log10Abf: Numeric. Log base 10 of the approximate Bayes factor.

Examples

if (FALSE) { # \dontrun{
result <- tagVariantsAndStudiesForIndexVariant(variant_id = "1_109274968_G_T")
result <- tagVariantsAndStudiesForIndexVariant(variant_id = "1_109274968_G_T"
    ,pageindex = 1, pagesize = 50)
    } # }