snpStats

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

SnpMatrix and XSnpMatrix classes and methods

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DOI: 10.18129/B9.bioc.snpStats

Bioconductor version: Development (3.23)

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 "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneticVariability, Microarray, SNP, Software

Version 1.61.0

In Bioconductor since BioC 2.8 (R-2.13) (14.5 years)

License GPL-3

Depends R (>= 2.10.0), survival, Matrix, methods

Imports graphics, grDevices, stats, utils, BiocGenerics

System Requirements

URL

Suggests hexbin

Linking To

Enhances

Depends On Me MAGAR

Imports Me cardelino, DExMA, gwascat, martini, RVS, scoreInvHap, dartR.base, GenomicTools.fileHandler, gpcp, GWASbyCluster, PhenotypeSimulator, TriadSim

Suggests Me crlmm, GenomicFiles, GWASTools, ldblock, omicRexposome, omicsPrint, VariantAnnotation, adjclust, dartR, dartR.popgen, genio, pegas, RcppDPR, statgenGWAS

Links To Me

Build Report Build Report

Package Archives

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

Source Package snpStats_1.61.0.tar.gz

Windows Binary (x86_64) snpStats_1.61.0.zip (64-bit only)

macOS Binary (x86_64) snpStats_1.61.0.tgz

macOS Binary (arm64) snpStats_1.61.0.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/

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