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Streamlined Tidy Data Access to Open Target Genetics GraphQL API

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Version

Install

install.packages('otargen')

Monthly Downloads

181

Version

1.1.5

License

MIT + file LICENSE

Maintainer

Amir Feizi

Last Published

September 22nd, 2024

Functions in otargen (1.1.5)

mousePhenotypesQuery

Retrieve Mouse Phenotypes data for a specified gene.
knownDrugsQuery

Retrieve Known Drugs data for a specified gene.
overlapInfoForStudy

Retrieves overlap info for a study and a list of studies
pheWAS

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

Retrieves tag variants and studies for a given index variant.
studyVariants

Retrieves all variants for a study.
run_custom_query

Running custom GraphQL queries
studyInfo

Retrieve study summary information.
gwasRegional

Retrieve GWAS summary statistics for a genomic region.
studyLocus2GeneTable

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

Retrieve GWAS credible set data
studiesAndLeadVariantsForGeneByL2G

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

Retrieve calculated QTL summary statistics for credible variant set.
topOverlappedStudies

Retrieve top studies having overlap in identified loci.
plot_l2g

Radar plot for L2G partial scores from studiesAndLeadVariantsForGeneByL2G()
qtlColocalisationVariantQuery

Retrieve QTL colocalisation results of a variant
variantInfo

Retrieves information about a variant.
plot_manhattan

Plot results from manhattan()
plot_phewas

Plot PheWAS() results.
clinvarQuery

Retrieve ClinVar data for a specified gene and disease.
getLociGenes

Retrieve summary information of the genes in a locus
compGenomicsQuery

Retrieve Comparative Genomics data for a specified gene.
chemblQuery

Retrieve ChEMBL data for a specified gene and disease.
genesForVariant

Retrieves variant-surrounding genes with calculated statistics for causal gene prioritization.
gwasColocalisation

Retrieve calculated GWAS colocalisation data
geneInfo

Retrieve gene summary information.
colocalisationsForGene

Retrieves Colocalisation Statistics for a Given Gene
gwasColocalisationForRegion

Retrieve GWAS colocalisation data for a genomic region .
geneticConstraintQuery

Retrieve Genetic Constraint data for a specified gene.
plot_coloc

Scatter plot of colocalisations for gene and reported traits.
indexVariantsAndStudiesForTagVariant

Retrieve population-level summary GWAS statistics.
manhattan

Retrieve GWAS summary statistics to create a Manhattan plot