Genomewide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for singlenucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multicore symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using IdentityByDescent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 classes and generic functions. The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls.
Package details 


Author  Xiuwen Zheng [aut, cre, cph], Stephanie Gogarten [ctb], Cathy Laurie [ctb], Bruce Weir [ctb, ths] 
Bioconductor views  Genetics Infrastructure PrincipalComponent StatisticalMethod 
Maintainer  Xiuwen Zheng <[email protected]> 
License  GPL3 
Version  1.12.2 
URL  http://github.com/zhengxwen/SNPRelate http://corearray.sourceforge.net/tutorials/SNPRelate/ 
Package repository  View on Bioconductor 
Installation 
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