title: R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment.
abstract: Phenome-wide association studies (PheWAS) have been used to replicate known genetic associations and discover new phenotype associations for genetic variants. This PheWAS implementation allows users to translate ICD-9 codes to PheWAS case and control groups, perform analyses using these and/or other phenotypes with covariate adjustments and plot the results. We demonstrate the methods by replicating a PheWAS on rs3135388 (near HLA-DRB, associated with multiple sclerosis) and performing a novel PheWAS using an individual's maximum white blood cell count (WBC) as a continuous measure. Our results for rs3135388 replicate known associations with more significant results than the original study on the same dataset. Our PheWAS of WBC found expected results, including associations with infections, myeloproliferative diseases and associated conditions, such as anemia. These results demonstrate the performance of the improved classification scheme and the flexibility of PheWAS encapsulated in this package.
  
  
  METHODS
  This R package is freely available under the Gnu Public License (GPL-3) from http://phewascatalog.org. It is implemented in native R and is platform independent.
authors.affiliation: Department of Biomedical Informatics and Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37212, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Carroll
authors.affiliation: Department of Biomedical Informatics and Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37212, USA.
authors.forename: Lisa
authors.initials: L
authors.lastname: Bastarache
authors.affiliation: Department of Biomedical Informatics and Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37212, USADepartment of Biomedical Informatics and Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37212, USA.
authors.forename: Joshua C
authors.initials: JC
authors.lastname: Denny
mesh_terms: D003627:Data Interpretation, Statistical; D056726:Genetic Association Studies / Q000379:methods*; D014644:Genetic Variation; D006801:Humans; D009103:Multiple Sclerosis / Q000235:genetics; D010641:Phenotype; D012984:Software
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