snpStats
This is the development version of snpStats; for the stable release version, see snpStats.
SnpMatrix and XSnpMatrix classes and methods
Bioconductor version: Development (3.24)
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("snpStats")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 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 | 1.63.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) (15.5 years) |
| License | GPL-3 |
| Depends | R (>= 2.10.0), survival, Matrix, methods |
| Imports | graphics, grDevices, stats, utils, BiocGenerics |
| System Requirements | |
| URL |
See More
| Suggests | hexbin |
| Linking To | |
| Enhances | |
| Depends On Me | MAGAR |
| Imports Me | cardelino, DExMA, gwascat, martini, RVS, scoreInvHap, GenomicTools.fileHandler, gpcp, GWASbyCluster, SNPkit, 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_1.63.0.tar.gz |
| Windows Binary (x86_64) | snpStats_1.63.0.zip |
| macOS Binary (big-sur-x86_64) | snpStats_1.63.0.tgz |
| macOS Binary (sonoma-arm64) | snpStats_1.63.0.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 |