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>

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

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

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