LocusXcanR: An R Shiny application for integrating TWAS results with other 'omics data

LocusXcanR is an R package that creates an R Shiny application to assist with TWAS fine-mapping. It allows researchers to integrate information from multiple sources (GWAS and TWAS) and interactively visualize TWAS results in-context, one genomic locus at a time. LocusXcanR aids TWAS interpretation, can be extended to other ‘omics data, and highlights R Shiny’s effectiveness at presenting results in an approachable, interactive, and visual format.

For additional details and an application of LocusXcanR, please reference our manuscript currently available on bioRxiv: https://www.biorxiv.org/content/10.1101/2021.02.23.432444v1

Source code available in R/app.R

Prerequisites

The LocusXcanR package depends on R (>= 4.0.3) and imports the following R packages:

• data.table
• dplyr
• DT
• ggplot2
• Gviz
• magrittr
• plotly
• RColorBrewer
• shiny
• stats
• tidyr
• visNetwork

How to install the package from GitHub

First, install the devtools package. You can do this from CRAN. Invoke R and then type:

install.packages("devtools")

Load the devtools package:

library(devtools)

Install the package from GitHub using install_github("author/package") as follows:

install_github("amanda-tapia/LocusXcanR")

Accessing LocusXcanR vignette

A vignette documenting the use of LocusXcanR is contained within the package. After installing the package, run:

vignette("LocusXcanR")

This should bring up the vignette in the help window of the R console. If this doesn't work, you may need to try the following:

   
  devtools::install(build_vignettes = TRUE)
  vignette("LocusXcanR")
  

Example scripts and data

See R/example/example_script.R to render an example R Shiny application.

Example datasets can be found in inst/extdata.