GWASTools

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see GWASTools.

Tools for Genome Wide Association Studies


Bioconductor version: 3.6

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

Author: Stephanie M. Gogarten, Cathy Laurie, Tushar Bhangale, Matthew P. Conomos, Cecelia Laurie, Michael Lawrence, Caitlin McHugh, Ian Painter, Xiuwen Zheng, Jess Shen, Rohit Swarnkar, Adrienne Stilp, Sarah Nelson

Maintainer: Stephanie M. Gogarten <sdmorris at uw.edu>, Adrienne Stilp <amstilp at uw.edu>

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

Installation

To install this package, start R (version "3.4") 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 PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneticVariability, Microarray, QualityControl, SNP, Software
Version 1.24.1
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
System Requirements
URL
See More
Suggests ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation
Linking To
Enhances
Depends On Me GWASdata
Imports Me GENESIS
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_1.24.1.tar.gz
Windows Binary GWASTools_1.24.1.zip
Mac OS X 10.11 (El Capitan) GWASTools_1.24.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/GWASTools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GWASTools
Package Short Url https://bioconductor.org/packages/GWASTools/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive