Package index • otargen

Query functions

colocalisationsForGene(): Retrieves Colocalisation Statistics for a Given Gene

genesForVariant(): Retrieves variant-surrounding genes with calculated statistics for causal gene prioritization.

gwasColocalisation(): Retrieve calculated GWAS colocalisation data

gwasColocalisationForRegion(): Retrieve GWAS colocalisation data for a genomic region .

gwasCredibleSet(): Retrieve GWAS credible set data

gwasRegional(): Retrieve GWAS summary statistics for a genomic region.

manhattan(): Retrieve GWAS summary statistics to create a Manhattan plot

overlapInfoForStudy(): Retrieves overlap info for a study and a list of studies

pheWAS(): Retrieve PheWAS (Phenome Wide Association Studies) data for a variant.

qtlColocalisationVariantQuery(): Retrieve QTL colocalisation results of a variant

qtlCredibleSet(): Retrieve calculated QTL summary statistics for credible variant set.

studiesAndLeadVariantsForGeneByL2G(): Retrieve "locus-to-gene" (L2G) model summary data for a gene.

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

tagVariantsAndStudiesForIndexVariant(): Retrieves tag variants and studies for a given index variant.

indexVariantsAndStudiesForTagVariant(): Retrieve population-level summary GWAS statistics.

topOverlappedStudies(): Retrieve top studies having overlap in identified loci.

getLociGenes(): Retrieve summary information of the genes in a locus

geneInfo(): Retrieve gene summary information.

studyInfo(): Retrieve study summary information.

variantInfo(): Retrieves information about a variant.

studyVariants(): Retrieves all variants for a study.

chemblQuery(): Retrieve ChEMBL data for a specified gene and disease.

clinvarQuery(): Retrieve ClinVar data for a specified gene and disease.

compGenomicsQuery(): Retrieve Comparative Genomics data for a specified gene.

geneticConstraintQuery(): Retrieve Genetic Constraint data for a specified gene.

knownDrugsQuery(): Retrieve Known Drugs data for a specified gene.

mousePhenotypesQuery(): Retrieve Mouse Phenotypes data for a specified gene.

Plotting functions

plot_coloc(): Scatter plot of colocalisations for gene and reported traits.

plot_l2g(): Radar plot for L2G partial scores from studiesAndLeadVariantsForGeneByL2G()

plot_manhattan(): Plot results from manhattan()

plot_phewas(): Plot PheWAS() results.

Custom query function

run_custom_query(): Running custom GraphQL queries