mgwasr

https://github.com/xia-lab/mgwasr

Repository

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/",
  out.width = "100%"
)
```

# mGWASR 

#### A companion R package for the mGWAS-Explorer web server

## Description

**mGWASR** contains the R functions and libraries underlying the [mGWAS-Explorer](https://www.mgwas.ca/) 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.

``` r
if (!requireNamespace("pacman", quietly = TRUE)) {
  install.packages("pacman")
}
if (!requireNamespace("devtools", quietly = TRUE)) {
  install.packages("devtools")
}

library(pacman)
library(devtools)

# need to update the depdencies
pacman::p_load(RSQLite, igraph, BiocManager, BiocParallel,  pryr,  httr,  reshape,  ggplot2,  RJSONIO,  RCurl,  XML,  ggforce,  graphlayouts,  compiler,  dplyr,  RColorBrewer,  Cairo,  plyr,  qs,  rjson,  TwoSampleMR,
               mygene, myvariant, RMySQL, MendelianRandomization, VariantAnnotation)
devtools::install_github(c(
  "mglev1n/ldscr",
  "boxiangliu/locuscomparer",
  "explodecomputer/plinkbinr",
  "MRCIEU/genetics.binaRies",
  "mrcieu/gwasvcf",
  "mrcieu/gwasglue"
))
```

### 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:

``` r
# 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)

# 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:

``` r
vignette(package="mGWASR")
```

Within a web-browser:

``` r
browseVignettes("mGWASR")
```

## Citation

mGWASR has been developed by the [Xia Lab](http://xialab.ca/) at McGill University. The original manuscript (web-based version) can be found [here](https://www.mdpi.com/2218-1989/12/6/526).

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. 

## 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

Owner

Citation (CITATION.cff)

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.3.0
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "mGWASR" in publications use:'
type: software
license: MIT
title: 'mGWASR: A companion R package for the mGWAS-Explorer web server'
version: 0.0.0.9000
doi: 10.3390/metabo12060526
abstract: This package contains the entire underlying R functionality of the web-based
  tool mGWAS-Explorer.
authors:
- family-names: Chang
  given-names: Le
  email: le.chang@mail.mcgill.ca
  orcid: https://orcid.org/0000-0002-0966-7923
- family-names: Xia
  given-names: Jianguo
  email: jeff.xia@mcgill.ca
  orcid: https://orcid.org/0000-0003-2040-2624
preferred-citation:
  type: article
  title: 'mGWAS-Explorer: Linking SNPs, Genes, Metabolites, and Diseases for Functional
    Insights'
  authors:
  - family-names: Chang
    given-names: Le
    email: le.chang@mail.mcgill.ca
    orcid: https://orcid.org/0000-0002-0966-7923
  - family-names: Xia
    given-names: Jianguo
    email: jeff.xia@mcgill.ca
    orcid: https://orcid.org/0000-0003-2040-2624
  year: '2022'
  journal: Metabolites
  url: https://www.mdpi.com/2218-1989/12/6/526
  doi: 10.3390/metabo12060526
contact:
- family-names: Chang
  given-names: Le
  email: le.chang@mail.mcgill.ca
  orcid: https://orcid.org/0000-0002-0966-7923
references:
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=testthat
  version: '>= 3.0.0'

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