studyVariants: Retrieves all variants for a study.

In otargen: Access Open Target Genetics

Retrieves all variants for a study.

Description

For an input study ID, this function returns information of all variants across associated loci. The output also includes information about the associated genes within the each loci.

Usage

studyVariants(study_id)

Arguments

study_id

Character: Study ID(s) generated by Open Targets Genetics (e.g GCST90002357).

Value

Returns a list of two data frames.

the first data frame (tibble format) includes the loci data frame with following data structure:

• variant.id: Character. Variant ID.

• pval: Numeric. P-value.

• variant.nearestCodingGene.symbol: Character. Symbol of the nearest coding gene to the variant.

• variant.rsId: Character. Variant rsID.

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

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

• variant.nearestCodingGeneDistance: Integer. Distance to the nearest coding gene.

• credibleSetSize: Integer. Size of the credible set.

• ldSetSize: Integer. Size of the LD set.

• oddsRatio: Numeric. Odds ratio.

• beta: Numeric. Beta value.

The second data frame includes gene information with following data structure:

• score: Numeric. Gene score.

• gene.id: Character. Gene ID.

• gene.symbol: Character. Gene symbol.

Examples

## Not run: 
result <- studyVariants(study_id = "GCST003155")

## End(Not run)

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