The R package switchgrassGWAS provides functions for genome-wide association analysis on the Panicum virgatum diversity (pvdiv) panel. It’s associated with this paper.
You can install the development version from GitHub from within R:
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") devtools::install_github("Alice-MacQueen/switchgrassGWAS")
Installations for additional functionality
Some switchgrassGWAS functions require the installation of additional packages.
These packages can be installed from within R with:
install.packages("bigsnpr") install.packages("mashr") devtools::install_github("lcolladotor/dots") if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") install.packages("curl") BiocManager::install(c("GenomicFeatures", "VariantAnnotation"))
The switchgrass (Panicum virgatum) diversity panel, the pvdiv panel, is being grown at many common gardens across the United States and Mexico. Many researchers are measuring phenotypes on this panel to understand the genes and genetic regions affecting these phenotypes.
This package provides the code for fast, less memory intensive genome-wide association (GWAS) using bigsnpr. It also provides functions to link diversity panel phenotypic data with publicly available SNP data, to prepare GWAS results plots using ggplot, and to prepare multiple univariate GWAS results for use in the downstream application mash.
Download the SNP data here.
The HTML documentation for the development version is available on Github.
Citing this work
If you find the switchgrassGWAS package or any of the source code in this repository useful for your work, please cite:
Lovell, J.T., MacQueen, A.H., Mamidi, S. et al. Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature (2021). https://doi.org/10.1038/s41586-020-03127-1