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>

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

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

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