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SnpMatrix and XSnpMatrix classes and methods

Bioconductor version: Release (3.19)

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 "4.4") and enter:

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


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:

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


biocViews GeneticVariability, Microarray, SNP, Software
Version 1.54.0
In Bioconductor since BioC 2.8 (R-2.13) (13.5 years)
License GPL-3
Depends R (>= 2.10.0), survival, Matrix, methods
Imports graphics, grDevices, stats, utils, BiocGenerics, zlibbioc
System Requirements
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Suggests hexbin
Linking To
Depends On Me MAGAR
Imports Me cardelino, DExMA, GeneGeneInteR, gwascat, martini, RVS, scoreInvHap, GenomicTools.fileHandler, GWASbyCluster, PhenotypeSimulator, TriadSim
Suggests Me crlmm, GenomicFiles, GWASTools, ldblock, omicRexposome, omicsPrint, VariantAnnotation, adjclust, dartR, dartR.base, dartR.popgen, genio, pegas, statgenGWAS
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package snpStats_1.54.0.tar.gz
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macOS Binary (x86_64) snpStats_1.54.0.tgz
macOS Binary (arm64) snpStats_1.54.0.tgz
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Source Repository (Developer Access) git clone
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