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To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("SNPRelate")
In most cases, you don't need to download the package archive at all.
SNPRelate
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Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Bioconductor version: Release (3.1)
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 format in this package is also used by the GWASTools package with the support of S4 classes and generic functions.
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 and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("SNPRelate")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SNPRelate")
| HTML | R Script | Tutorials for the R/Bioconductor Package SNPRelate |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Genetics, Infrastructure, PrincipalComponent, Software, StatisticalMethod |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (1 year) |
| License | GPL-3 |
| Depends | R (>= 2.14), gdsfmt(>= 1.2.2) |
| Imports | |
| LinkingTo | gdsfmt |
| Suggests | parallel, RUnit, knitr, MASS, BiocGenerics |
| SystemRequirements | |
| Enhances | |
| URL | http://github.com/zhengxwen/SNPRelate http://corearray.sourceforge.net/tutorials/SNPRelate/ |
| BugReports | http://github.com/zhengxwen/SNPRelate/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | GENESIS, GWASTools, HIBAG |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SNPRelate_1.2.0.tar.gz |
| Windows Binary | SNPRelate_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | SNPRelate_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | SNPRelate_1.2.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/SNPRelate/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/SNPRelate/ |
| Package Downloads Report | Download Stats |
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