GWASTools

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see GWASTools.

Tools for Genome Wide Association Studies

Bioconductor version: 3.18

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

Author: Stephanie M. Gogarten [aut], Cathy Laurie [aut], Tushar Bhangale [aut], Matthew P. Conomos [aut], Cecelia Laurie [aut], Michael Lawrence [aut], Caitlin McHugh [aut], Ian Painter [aut], Xiuwen Zheng [aut], Jess Shen [aut], Rohit Swarnkar [aut], Adrienne Stilp [aut], Sarah Nelson [aut], David Levine [aut], Sonali Kumari [ctb] (Converted vignettes from Sweave to RMarkdown / HTML.), Stephanie M. Gogarten [cre]

Maintainer: Stephanie M. Gogarten <sdmorris at uw.edu>

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

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("GWASTools")

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("GWASTools")

Data formats in GWASTools	PDF	R Script
GWAS Data Cleaning	PDF	R Script
Preparing Affymetrix Data	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneticVariability, Microarray, QualityControl, SNP, Software
Version	1.48.0
In Bioconductor since	BioC 2.9 (R-2.14) (12.5 years)
License	Artistic-2.0
Depends	Biobase
Imports	graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table
System Requirements
URL	https://github.com/smgogarten/GWASTools

Suggests	ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr
Linking To
Enhances
Depends On Me	GWASdata, mBPCR
Imports Me	GENESIS, gwasurvivr
Suggests Me	podkat
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	GWASTools_1.48.0.tar.gz
Windows Binary	GWASTools_1.48.0.zip
macOS Binary (x86_64)	GWASTools_1.48.0.tgz
macOS Binary (arm64)	GWASTools_1.48.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GWASTools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GWASTools
Bioc Package Browser	https://code.bioconductor.org/browse/GWASTools/
Package Short Url	https://bioconductor.org/packages/GWASTools/
Package Downloads Report	Download Stats