mGWASR 
A companion R package for the mGWAS-Explorer web server
Description
mGWASR contains the R functions and libraries underlying the mGWAS-Explorer web server. After installing and loading the package, users will be able to reproduce the same results from their local computers using the corresponding R command history downloaded from mGWAS-Explorer, thereby achieving maximum flexibility and reproducibility.
Getting Started
Step 1. Install package dependencies
To use mGWASR , first install all package dependencies. Ensure that you are able to download packages from bioconductor. To install package dependencies, use the pacman R package (for those with >R 3.5.1). Note that some of these packages may require additional library dependencies that need to be installed prior to their own successful installation.
install.packages("pacman")
library(pacman)
# need to update the depdencies
pacman::p_load(RSQLite, igraph, BiocParallel, pryr, httr, reshape, ggplot2, RJSONIO, RCurl, XML, ggforce, graphlayouts, compiler, dplyr, RColorBrewer, Cairo, plyr, qs, rjson, TwoSampleMR)Step 2. Install the package
mGWASR is freely available from GitHub. The package documentation, including the vignettes for each module and user manual is available within the downloaded R package file. If all package dependencies were installed, you will be able to install the mGWASR. Due to issues with Latex, some users may find that they are only able to install mGWASR without any documentation (i.e. vignettes).
Install the package directly from github using the devtools package. Open R and enter:
# Step 1: Install devtools
install.packages("devtools")
library(devtools)
# Step 2: Install mGWASR WITHOUT documentation
devtools::install_github("xia-lab/mGWASR", build = TRUE, build_opts = c("--no-resave-data", "--no-manual", "--no-build-vignettes"), force = TRUE)
# Step 2: Install mGWASR WITH documentation
devtools::install_github("xia-lab/mGWASR", build = TRUE, build_opts = c("--no-resave-data", "--no-manual"), build_vignettes = TRUE, force = TRUE)Tutorials
For detailed tutorials on how to use mGWASR, please refer to the R package vignettes. Note, the functions below work only if the R package vignettes were built.
Within R:
vignette(package="mGWASR")Within a web-browser:
browseVignettes("mGWASR")Citation
mGWASR has been developed by the Xia Lab at McGill University. The original manuscript (web-based version) can be found here.
We encourage users to further develop the package to suit their needs. If you use the R package, please cite us:
Chang, L., Zhou, G., & Xia, J. (2023). mGWAS-Explorer 2.0: causal analysis and interpretation of metabolite-phenotype associations. Under review
Chang, L., Zhou, G., Ou, H., & Xia, J. (2022). mGWAS-Explorer: Linking SNPs, Genes, Metabolites, and Diseases for Functional Insights. Metabolites, 12(6), 526. https://doi.org/10.3390/metabo12060526
Bugs or feature requests
To inform us of any bugs or requests, please open a new issue or send an email to le.chang @ mail.mcgill.ca