This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

snpStats

This is the development version of snpStats; for the stable release version, see snpStats.

SnpMatrix and XSnpMatrix classes and methods

Bioconductor version: Development (3.18)

Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

Author: David Clayton <dc208 at cam.ac.uk>

Maintainer: David Clayton <dc208 at cam.ac.uk>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("snpStats")

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("snpStats")
Data input PDF R Script
Fst PDF R Script
Imputation and meta-analysis PDF R Script
LD statistics PDF R Script
Principal components analysis PDF R Script
snpMatrix-differences PDF
snpStats introduction PDF R Script
TDT tests PDF R Script
Reference Manual PDF

Details

biocViews GeneticVariability, Microarray, SNP, Software
Version 1.51.0
In Bioconductor since BioC 2.8 (R-2.13) (12.5 years)
License GPL-3
Depends R (>= 2.10.0), survival, Matrix, methods
Imports graphics, grDevices, stats, utils, BiocGenerics, zlibbioc
Linking To
Suggests hexbin
System Requirements
Enhances
URL
See More
Depends On Me MAGAR
Imports Me cardelino, DExMA, GeneGeneInteR, gwascat, martini, RVS, scoreInvHap
Suggests Me crlmm, GenomicFiles, GWASTools, ldblock, omicRexposome, omicsPrint, VariantAnnotation
Links To Me
Build Report  

Package Archives

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

Source Package snpStats_1.51.0.tar.gz
Windows Binary snpStats_1.51.0.zip (64-bit only)
macOS Binary (x86_64) snpStats_1.51.0.tgz
macOS Binary (arm64) snpStats_1.51.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/snpStats
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/snpStats
Bioc Package Browser https://code.bioconductor.org/browse/snpStats/
Package Short Url https://bioconductor.org/packages/snpStats/
Package Downloads Report Download Stats