snpStats
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 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 "4.4") and enter:
if (!require("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")
Data input | R Script | |
Fst | R Script | |
Imputation and meta-analysis | R Script | |
LD statistics | R Script | |
Principal components analysis | R Script | |
snpMatrix-differences | ||
snpStats introduction | R Script | |
TDT tests | R Script | |
Reference Manual |
Details
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 | |
URL |
See More
Suggests | hexbin |
Linking To | |
Enhances | |
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 | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | snpStats_1.54.0.tar.gz |
Windows Binary | snpStats_1.54.0.zip (64-bit only) |
macOS Binary (x86_64) | snpStats_1.54.0.tgz |
macOS Binary (arm64) | snpStats_1.54.0.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/ |
Package Downloads Report | Download Stats |