otargen (version 1.1.5)

studyLocus2GeneTable: Retrieve the locus-to-gene (L2G) data table for loci genes.

Description

This function fetches the locus-to-gene (L2G) pipeline summary data table for the neighboring genes of a variant in a GWAS study.

Usage

studyLocus2GeneTable(study_id, variant_id)

Value

Returns a data frame with the summary statistics of the study and a data table containing various calculated scores and features for any lead variant. The output table has the following data structure:

• studyId: Character. Study ID.

• variant.id: Character. Variant ID.

• variant.rsId: Character. Variant rsID.

• yProbaDistance: Numeric. Distance score.

• yProbaModel: Numeric. Model score.

• yProbaMolecularQTL: Numeric. Molecular QTL score.

• yProbaPathogenicity: Numeric. Pathogenicity score.

• yProbaInteraction: Numeric. Interaction score.

• hasColoc: Logical. Indicates if colocalization data is available.

• distanceToLocus: Numeric. Distance to the locus.

• gene.id: Character. Gene ID.

• gene.symbol: Character. Gene symbol.

Arguments

study_id

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

variant_id

Character: generated ID for variants by Open Targets Genetics (e.g. 1_154119580_C_A) or rsId (rs2494663).

Examples

if (FALSE) {
result <- studyLocus2GeneTable(study_id = "GCST90002357", variant_id = "1_154119580_C_A")
result <- studyLocus2GeneTable(study_id = "GCST90002357", variant_id = "rs2494663")
}