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Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Bioconductor version: Release (3.19)

Genome-wide 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 single-nucleotide 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 multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent 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 in whole-genome and whole-exome variant data.

Author: Xiuwen Zheng [aut, cre, cph] , Stephanie Gogarten [ctb], Cathy Laurie [ctb], Bruce Weir [ctb, ths]

Maintainer: Xiuwen Zheng <zhengx at>

Citation (from within R, enter citation("SNPRelate")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

SNPRelate Tutorial HTML R Script
Reference Manual PDF


biocViews Genetics, Infrastructure, PrincipalComponent, Software, StatisticalMethod
Version 1.38.0
In Bioconductor since BioC 3.0 (R-3.1) (10 years)
License GPL-3
Depends R (>= 2.15), gdsfmt(>= 1.8.3)
Imports methods
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Suggests parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics
Linking To gdsfmt
Enhances SeqArray(>= 1.12.0)
Depends On Me RAIDS, SeqSQC
Imports Me CNVRanger, GDSArray, GENESIS, gwasurvivr, VariantExperiment, EthSEQ, gwid, simplePHENOTYPES
Suggests Me GWASTools, HIBAG, SAIGEgds, SeqArray, snplinkage
Links To Me
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Source Package SNPRelate_1.38.0.tar.gz
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