View source: R/studyLocus2GeneTable.R
studyLocus2GeneTable | R Documentation |
This function fetches the locus-to-gene (L2G) pipeline summary data table for the neighboring genes of a variant in a GWAS study.
studyLocus2GeneTable(study_id, variant_id)
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). |
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.
## Not run:
result <- studyLocus2GeneTable(study_id = "GCST90002357", variant_id = "1_154119580_C_A")
result <- studyLocus2GeneTable(study_id = "GCST90002357", variant_id = "rs2494663")
## End(Not run)
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