snpStats

DOI: 10.18129/B9.bioc.snpStats    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see snpStats.

SnpMatrix and XSnpMatrix classes and methods

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

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

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")

 

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

Details

biocViews	GeneticVariability, Microarray, SNP, Software
Version	1.34.0
In Bioconductor since	BioC 2.8 (R-2.13) (8.5 years)
License	GPL-3
Depends	R (>= 2.10.0), survival, Matrix, methods
Imports	graphics, grDevices, stats, utils, BiocGenerics, zlibbioc
LinkingTo
Suggests	hexbin
SystemRequirements
Enhances
URL
Depends On Me	eQTL, GGBase, GGdata
Imports Me	FunciSNP, GeneGeneInteR, GGtools, gQTLstats, ldblock, martini, RVS, scoreInvHap
Suggests Me	crlmm, gwascat, GWASTools, omicRexposome, omicsPrint, VariantAnnotation
Links To Me
Build Report

Package Archives

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

Source Package	snpStats_1.34.0.tar.gz
Windows Binary	snpStats_1.34.0.zip
Mac OS X 10.11 (El Capitan)	snpStats_1.33.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/snpStats
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/snpStats
Package Short Url	https://bioconductor.org/packages/snpStats/
Package Downloads Report	Download Stats