DOI: 10.18129/B9.bioc.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>

Maintainer: David Clayton <dc208 at>

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


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

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script 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 snpMatrix-differences
PDF R Script snpStats introduction
PDF R Script TDT tests
PDF   Reference Manual


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
Suggests hexbin
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
macOS Binary (x86_64) snpStats_1.51.0.tgz
macOS Binary (arm64) snpStats_1.51.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

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