mirApp

Shiny app to plot SNPs modulating microRNA-gene interactions in tumors throughout the genome

PREREQUISITES

• Must have R installed on your local machine. To install R, go to https://cran.r-project.org/mirrors.html and choose the mirror closest to your local. Follow the instructions for installation.

• Once installed, open R and install packages "shiny" and "ggplot2". To install packages, type in the R prompt:

>install.packages(c("shiny", "ggplot2"))

Allow R to install any package dependencies.

• Install RStudio to run the app. To install RStudio, go to https://www.rstudio.com/products/rstudio/download/ and follow the instructions for your operating system.

GETTING STARTED

• Download mirApp.tar.gz and untar it into whichever local directory you wish. To untar, type tar -xvzf mirApp.tar.gz in terminal or decompress using your software of choice.

• What lives here:

  • app.R Shiny app code including UX and server side functions
  • data/ directory containing all data files for running Shiny app.

• NOTE! Data files are not included in the repo due to their size. Data files can be downloaded from https://northwestern.box.com/s/co7kzy6qo7c5dlwbilapnocg34j7zjiv and should be placed in the data/ subdirectory.

RUNNING APP

• Open RStudio and set your working directory to the mirApp path location. To change your working directory in R, type in the R prompt: >setwd("path/to/mirApp") and replace "path/to/mirApp/" to your path.

• In RStudio, open app.R. In the top right corner of the code editor, press the "Run App" dropdown menu and run "Run in Window".

• When running the app, a window will appear. In the left panel, you must choose a cancer type in the dropdown menu, and a miRNA. miRNA names must follow TCGA convention. An explanation is provided in the "About" tab. Delete the instructions within the window before typing in your miRNA name.

• The plots will appear in the "Plot" tab. Because the data is very large, the app may be slow and may take time to generate the figures. Please be patient!

• If the app returns an error after your inputs (cancer type and miRNA name), this means that the miRNA is unconsidered within the cancer type in the study.

FULL RESULTS TABLES (without using Shiny)

• Full tables of the regQTL analysis results for all trios may be downloaded as tab-separated files from https://northwestern.app.box.com/s/jpmzlsrbnlilk5lm5i7mp9fyrmawdgih