Access Open Target Genetics

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Documentation for package ‘otargen’ version 1.1.1

• DESCRIPTION file.
• Package NEWS.

Help Pages

colocalisationsForGene	Retrieves Colocalisation Statistics for a Given Gene
geneInfo	Retrieve gene summary information.
genesForVariant	Retrieves variant-surrounding genes with calculated statistics for causal gene prioritization.
getLociGenes	Retrieve summary information of the genes in a locus
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.
indexVariantsAndStudiesForTagVariant	Retrieve population-level summary GWAS statistics.
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.
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.
qtlColocalisationVariantQuery	Retrieve QTL colocalisation results of a variant
qtlCredibleSet	Retrieve calculated QTL summary statistics for credible variant set.
run_custom_query	Running custom GraphQL queries
studiesAndLeadVariantsForGeneByL2G	Retrieve "locus-to-gene" (L2G) model summary data for a gene.
studyInfo	Retrieve study summary information.
studyLocus2GeneTable	Retrieve the locus-to-gene (L2G) data table for loci genes.
studyVariants	Retrieves all variants for a study.
tagVariantsAndStudiesForIndexVariant	Retrieves tag variants and studies for a given index variant.
topOverlappedStudies	Retrieve top studies having overlap in identified loci.
variantInfo	Retrieves information about a variant.