title: traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals.
abstract: Genome-wide association studies (GWASs) have successfully identified many sequence variants that are significantly associated with common diseases and traits. Tens of thousands of such trait-associated SNPs have already been cataloged, which we believe form a great resource for genomic research. Recent studies have demonstrated that the collection of trait-associated SNPs can be exploited to indicate whether a given genomic interval or intervals are likely to be functionally connected with certain phenotypes or diseases. Despite this importance, currently, there is no ready-to-use computational tool able to connect genomic intervals to phenotypes. Here, we present traseR, an easy-to-use R Bioconductor package that performs enrichment analyses of trait-associated SNPs in arbitrary genomic intervals with flexible options, including testing method, type of background and inclusion of SNPs in LD.
  
  
  
  The traseR R package preloaded with up-to-date collection of trait-associated SNPs are freely available in Bioconductor
  
  
  
  zhaohui.qin@emory.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Mathematics and Computer Science.
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.affiliation: Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA and Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA 30322, USA.
authors.forename: Zhaohui S
authors.initials: ZS
authors.lastname: Qin
mesh_terms: D055106:Genome-Wide Association Study; D023281:Genomics; D006801:Humans; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012984:Software