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_oiandassocgr_from_db. make_oiproduces an ontologyIndex to simplify visualization and traversal of ontological hierarchies.assocgr_from_dbproduces a GRanges representation of the GWAS catalog to simplify interrogation of GWAS hits in genomic coordinates.