GWASTools

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see GWASTools.

Tools for Genome Wide Association Studies

Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneticVariability, Microarray, QualityControl, SNP, Software

Version 1.30.1

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 https://github.com/smgogarten/GWASTools

Suggests ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation

Linking To

Enhances

Depends On Me GWASdata

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_1.30.1.tar.gz

Windows Binary GWASTools_1.30.1.zip

Mac OS X 10.11 (El Capitan) GWASTools_1.30.1.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

Old Source Packages for BioC 3.9 Source Archive