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 (!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 | 1.34.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) (13 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 | 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 | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/snpStats/ |
| Package Short Url | https://bioconductor.org/packages/snpStats/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |