SNPRelate

DOI: 10.18129/B9.bioc.SNPRelate    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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")

 

HTML	R Script	SNPRelate Tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	Genetics, Infrastructure, PrincipalComponent, Software, StatisticalMethod
Version	1.30.1
In Bioconductor since	BioC 3.0 (R-3.1) (8 years)
License	GPL-3
Depends	R (>= 2.15), gdsfmt(>= 1.8.3)
Imports	methods
LinkingTo	gdsfmt
Suggests	parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics
SystemRequirements
Enhances	SeqArray(>= 1.12.0)
URL	http://github.com/zhengxwen/SNPRelate
BugReports	http://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

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SNPRelate_1.30.1.tar.gz
Windows Binary	SNPRelate_1.30.1.zip
macOS Binary (x86_64)	SNPRelate_1.30.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SNPRelate
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SNPRelate
Package Short Url	https://bioconductor.org/packages/SNPRelate/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.15	Source Archive