SNPRelate
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Bioconductor version: Release (3.17)
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("SNPRelate")):
Installation
To install this package, start R (version "4.3") 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")| SNPRelate Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Genetics, Infrastructure, PrincipalComponent, Software, StatisticalMethod |
| Version | 1.34.1 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9 years) |
| License | GPL-3 |
| Depends | R (>= 2.15), gdsfmt(>= 1.8.3) |
| Imports | methods |
| Linking To | gdsfmt |
| Suggests | parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics |
| System Requirements | |
| Enhances | SeqArray(>= 1.12.0) |
| URL | https://github.com/zhengxwen/SNPRelate |
| Bug Reports | https://github.com/zhengxwen/SNPRelate/issues |
See More
| 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_1.34.1.tar.gz |
| Windows Binary | SNPRelate_1.34.1.zip |
| macOS Binary (x86_64) | SNPRelate_1.34.1.tgz |
| macOS Binary (arm64) | SNPRelate_1.34.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SNPRelate |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SNPRelate |
| Bioc Package Browser | https://code.bioconductor.org/browse/SNPRelate/ |
| Package Short Url | https://bioconductor.org/packages/SNPRelate/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |