GWASTools

DOI: 10.18129/B9.bioc.GWASTools    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see GWASTools.

Tools for Genome Wide Association Studies

Bioconductor version: 3.13

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, David Levine

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

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews GeneticVariability, Microarray, QualityControl, SNP, Software
Version 1.38.0
In Bioconductor since BioC 2.9 (R-2.14) (10 years)
License Artistic-2.0
Depends Biobase
Imports graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table
LinkingTo
Suggests ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel
SystemRequirements
Enhances
URL https://github.com/smgogarten/GWASTools
Depends On Me GWASdata, mBPCR
Imports Me GENESIS, gwasurvivr
Suggests Me podkat
Links To Me
Build Report  

Package Archives

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

Source Package GWASTools_1.38.0.tar.gz
Windows Binary GWASTools_1.38.0.zip
macOS 10.13 (High Sierra) GWASTools_1.38.0.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

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