Bioconductor – SNPRelate

DOI: 10.18129/B9.bioc.SNPRelate  

 

This package is for version 3.12 of Bioconductor;
for the stable, up-to-date release version, see
SNPRelate.

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

Bioconductor version: 3.12

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 u.washington.edu>

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

Installation

To install this package, start R (version
“4.0”) and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SNPRelate")

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

Documentation

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

browseVignettes("SNPRelate")

 

Details

biocViews Genetics, Infrastructure, PrincipalComponent, Software, StatisticalMethod
Version 1.24.0
In Bioconductor since BioC 3.0 (R-3.1) (6.5 years)
License GPL-3
Depends R (>= 2.15), gdsfmt(>= 1.8.3)
Imports methods
LinkingTo gdsfmt
Suggests parallel, Matrix, RUnit, knitr, MASS, BiocGenerics
SystemRequirements
Enhances SeqArray(>= 1.12.0)
URL github.com/zhengxwen/SNPRelate
BugReports github.com/zhengxwen/SNPRelate/issues
Depends On Me SeqSQC
Imports Me CNVRanger, GDSArray, GENESIS, gwasurvivr, VariantExperiment
Suggests Me GWASTools, HIBAG, SAIGEgds, SeqArray
Links To Me
Build Report  

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