View source: R/qtlColocalisationVariantQuery.R
qtlColocalisationVariantQuery | R Documentation |
The colocalisation analysis in Open Target Genetics is performed using the coloc method (Giambartolomei et al., 2014). Coloc is a Bayesian method which, for two traits, integrates evidence over all variants at a locus to evaluate the following hypotheses: - H0: No association with either trait - H1: Association with trait 1, not with trait 2 - H2: Association with trait 2, not with trait 1 - H3: Association with trait 1 and trait 2, two independent SNPs - H4: Association with trait 1 and trait 2, one shared SNP This analysis tests whether two independent associations at the same locus are consistent with having a shared causal variant. Colocalisation of two independent associations from two GWAS studies may suggest a shared causal mechanism.
qtlColocalisationVariantQuery(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 of the colocalisation information for a lead variant in a specific study. The output is a tidy data frame with the following data structure:
qtlStudyName
: Character vector. QTL study name.
phenotypeId
: Character vector. Phenotype ID.
gene.id
: Character vector. Gene ID.
gene.symbol
: Character vector. Gene symbol.
name
: Character vector. Tissue name.
indexVariant.id
: Character vector. Index variant ID.
indexVariant.rsId
: Character vector. Index variant rsID.
beta
: Numeric. Beta value.
h4
: Numeric. h4 value.
h3
: Numeric. h3 value.
log2h4h3
: Numeric. Log2(h4/h3) value.
## Not run:
result <- qtlColocalisationVariantQuery(study_id = "GCST90002357", variant_id = "1_154119580_C_A")
result <- qtlColocalisationVariantQuery(study_id = "GCST90002357", variant_id = "rs2494663")
## End(Not run)
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