indexVariantsAndStudiesForTagVariant: Retrieve population-level summary GWAS statistics.

In otargen: Access Open Target Genetics

Retrieve population-level summary GWAS statistics.

Description

For an input tag variant ID, this function returns a data frame(tibble format) with population-level summary statistics data across various GWAS studies.

Usage

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

Arguments

variant_id	Character: generated ID for variants by Open Targets Genetics (e.g. 1_154119580_C_A) or rsId (rs2494663).
pageindex	Integer: Index of the current page, pagination index >= 0.
pagesize	Integer: Number of records in a page, pagination size > 0.

Value

Returns a data frame containing the variant associated with the input tag variant. The table consists of the following columns:

• index_variant: Data frame. Data frame of index variants with the following columns:

  • id: Character vector. Variant ID.

  • rsId: Character vector. rsID of the variant.

• study: Data frame. Data frame of studies with the following columns:

  • studyId: Character vector. Study identifier.

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

  • traitCategory: Character vector. Trait category.

• pval: Numeric vector. P-value.

• pval_mantissa: Numeric vector. Mantissa of the p-value.

• pval_exponent: Integer vector. Exponent of the p-value.

• n_total: Integer vector. Total number of samples.

• n_cases: Integer vector. Number of cases.

• overall_r2: Numeric vector. Overall R-squared value.

• afr1000g_prop: Numeric vector. Proportion in African population in 1000 Genomes.

• amr1000g_prop: Numeric vector. Proportion in Admixed American population in 1000 Genomes.

• eas1000g_prop: Numeric vector. Proportion in East Asian population in 1000 Genomes.

• eur1000g_prop: Numeric vector. Proportion in European population in 1000 Genomes.

• sas1000g_prop: Numeric vector. Proportion in South Asian population in 1000 Genomes.

• log10abf: Numeric vector. Log10 ABF (Approximate Bayes Factor).

• posterior_probability: Numeric vector. Posterior probability.

• odds_ratio: Numeric vector. Odds ratio.

• odds_ratio_ci_lower: Numeric vector. Lower confidence interval of the odds ratio.

• odds_ratio_ci_upper: Numeric vector. Upper confidence interval of the odds ratio.

• beta: Numeric vector. Beta value.

• beta_ci_lower: Numeric vector. Lower confidence interval of the beta value.

• beta_ci_upper: Numeric vector. Upper confidence interval of the beta value.

• direction: Character vector. Direction of the effect.

Examples

## Not run: 
result <- indexVariantsAndStudiesForTagVariant(variant_id = "1_109274968_G_T")
result <- indexVariantsAndStudiesForTagVariant(variant_id = "rs12740374",
 pageindex = 1, pagesize = 50)

## End(Not run)

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