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gwasCatSearch

An R package to provide free text search, and ontology lookup for GWAS Catalog phenotypes

To install the package, use BiocManager::install("ccb-hms/gwasCatSearch").

A shiny app is available at https://vjcitn.shinyapps.io/gwasCatSearch.

The representation of the EBI GWAS catalog used in this package is managed at Harvard Medical School Center for Computational Biomedicine.

  • gwasCatSearch redistributes a compressed SQLite database that includes extracts from the Semantic SQL reprsentation of the Experimental Factor Ontology, along with extracts from the EBI GWAS catalog.
  • To leverage existing R programming methods with the ontology and the GWAS catalog, we provide functions make_oi and assocgr_from_db.
  • make_oi produces an ontologyIndex to simplify visualization and traversal of ontological hierarchies.
  • assocgr_from_db produces a GRanges representation of the GWAS catalog to simplify interrogation of GWAS hits in genomic coordinates.