SNPRelate
R package: parallel computing toolset for relatedness and principal component analysis of SNP data
This project is maintained by zhengxwen
SNPRelate: Parallel computing toolset for relatedness and principal component analysis of SNP data
Features
Genome-wide association studies are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed SNPRelate (R package for multi-core symmetric multiprocessing computer architectures) to accelerate two key computations on SNP data: principal component analysis (PCA) and relatedness analysis using identity-by-descent measures. The kernels of our algorithms are written in C/C++ and highly optimized.
R Documents
Bioconductor Release Branch (v1.10.2): Tutorial, Help Documents
News
- supports the SeqArray GDS format defined in the SeqArray package, see the vignette.
Citation
Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS (2012). A High-performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. Bioinformatics. DOI: 10.1093/bioinformatics/bts606.