tagVariantsAndStudiesForIndexVariant: Retrieves tag variants and studies for a given index variant.

In otargen: Access Open Target Genetics

Retrieves tag variants and studies for a given index variant.

Description

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

## Not run: 
result <- tagVariantsAndStudiesForIndexVariant(variant_id = "1_109274968_G_T")
result <- tagVariantsAndStudiesForIndexVariant(variant_id = "1_109274968_G_T"
    ,pageindex = 1, pagesize = 50)
    
## End(Not run)

otargen documentation built on Sept. 30, 2024, 9:43 a.m.