studyLocus2GeneTable {otargen} | R Documentation |
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)
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). |
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.
Examples
## Not run:
result <- studyLocus2GeneTable(study_id = "GCST90002357", variant_id = "1_154119580_C_A")
result <- studyLocus2GeneTable(study_id = "GCST90002357", variant_id = "rs2494663")
## End(Not run)