title: SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations.
abstract: Next-generation sequencing has enabled the study of a comprehensive catalogue of genetic variants for their impact on various complex diseases. Numerous consortia studies of complex traits have publically released their summary association statistics, which have become an invaluable resource for learning the underlying biology, understanding the genetic architecture, and guiding clinical translations. There is great interest in the field in developing novel statistical methods for analyzing and interpreting results from these genotype-phenotype association studies. One popular platform for method development and data analysis is R. In order to enable these analyses in R, it is necessary to develop packages that can efficiently query files of summary association statistics, explore the linkage disequilibrium structure between variants, and integrate various bioinformatics databases. The complexity and scale of sequence datasets and databases pose significant computational challenges for method developers. To address these challenges and facilitate method development, we developed the R package SEQMINER for annotating and querying files of sequence variants (e.g., VCF/BCF files) and summary association statistics (e.g., METAL/RAREMETAL files), and for integrating bioinformatics databases. SEQMINER provides an infrastructure where novel methods can be distributed and applied to analyzing sequence datasets in practice. We illustrate the performance of SEQMINER using datasets from the 1000 Genomes Project. We show that SEQMINER is highly efficient and easy to use. It will greatly accelerate the process of applying statistical innovations to analyze and interpret sequence-based associations. The R package, its source code and documentations are available from http://cran.r-project.org/web/packages/seqminer and http://seqminer.genomic.codes/.
authors.affiliation: Department of Clinical Sciences, Quantitative Biomedical Research Center, Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zhan
authors.affiliation: Institute for Personalized Medicine, College of Medicine, Pennsylvania State University, Pennsylvania, Hershey, United States of America.|Division of Biostatistics, Department of Public Health Sciences, College of Medicine, Pennsylvania State University, Hershey, Pennsylvania, United States of America.
authors.forename: Dajiang J
authors.initials: DJ
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D016208:Databases, Factual; D056726:Genetic Association Studies / Q000379:methods*; D014644:Genetic Variation / Q000235:genetics; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D011381:Programming Languages; D017422:Sequence Analysis, DNA; D012984:Software
keywords: genome annotation; R; information retrieval; next-generation sequencing; statistical genetics