Manage local r script engine

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Contents

Setup R Engine

Array Studio supports local execution of several popular R packages using Omicsoft's R engine, as long as R 3.0 or above is installed on user's local machine.

Users can configure R executables and update these R packages in Tools | R Integration | Set R Script Engine.

SetLocalRScriptEngine 01.png


Update packages

The Setup R Engine window lists R scripts prepared by Omicsoft and users can also write their own scripts in Scripts Directory. The R functions prepared by Omicsoft can be installed/updated automatically by checking the boxes and clicking on "Update" button.

Update all packages.png


Install R locally

R integration logic

  • User will have their own R software installed, and the according packages(library) installed in their R software
  • User can setup the R Executable path in ArrayStudio, so the data from ArrayStudio will be parsed into this R software for analysis
  • ArrayStudio will provide a GUI for users to conveniently select which data to analyze, and all the parameters for these packages will be provided as an option, default values will be assigned, but user can customize these paramters
  • When user click Run or Send to Server, the data and parameters will be parsed into R and get analyzed
  • When the analysis is done in R, ArrayStudio will take the output from R and import the result back into ArrayStudio (with some modifications in some cases)
  • User can easily view the table data and plot data with further customization in ArrayStudio

Warning.png WARNING: For all of the packages mentioned in this wiki, user will need to install the according library in their R software first


Install R and RStudio

Without R, the Setup R Engine would look like the screenshot below:

Without R installed.png

To Install R: Open an internet browser and go to www.r-project.org. Click the "download R" link in the middle of the page under "Getting Started." Select a CRAN location (a mirror site) and click the corresponding link. Click on the "Download R for Windows" link at the top of the page. Click on the "install R for the first time" link at the top of the page. Click "Download R for Windows" and save the executable file somewhere on your computer. Run the .exe file and follow the installation instructions.

Download R binary.png

Now that R is installed, you need to download and install RStudio.

To Install RStudio Go to www.rstudio.com and click on the "Download RStudio" button. Click on "Download RStudio Desktop." Click on the version recommended for your system, or the latest Windows version, and save the executable file. Run the .exe file and follow the installation instructions.

Download rstudio binary.png

install dependencies and dev tools

Some packages or dependencies are essential for the packages used in ArrayStudio, users might need to install them manually, for example, to install "hash", simply run install.packages("hash") would do the job; For some packages like "stringi", users might need to compile from source or specify type, as shown in the screenshot below:

Install stringi.png


update lumi

After installing R and RStudio, use the following command within RStudio to install lumi and dependencies.

source("https://bioconductor.org/biocLite.R")
biocLite("lumi")

library(lumi)

Install lumi package.png

Go to ArrayStudio -> Tools -> R Integration -> Set R Script Engine, check the box in front of lumi, click Update button, the package and script will be updated automatically.

Update lumi AS script.png


update samr

The samr package has been removed from CRAN since Aug/2018, so users might need to download the source package to a local directory, and then install it from source.

Install samr.png


Update other R packages in ArrayStudio

For other packages, first install the correspond packages in R (RStudio), either through install.packages() or through biocLite()

source("https://bioconductor.org/biocLite.R")
biocLite("statmod")
biocLite("limma")
biocLite("vsn")
biocLite("lumi")
 
install.packages("stringi")
install.packages("foreign")
# biocLite("samr")

biocLite("impute")


library(lumi)
library(limma)
library(statmod)


After that, check the boxes in front of each package, and click Update, as what we did for Lumi.

potential installation issues

Sometimes, users might got errors when installing a package, i.e. "installation path not writeable, unable to update packages: foreign, Matrix"

type .libPaths() command in RStudio, you would get the library paths. As shown below, the second path is the directory where core libraries would be installed.

Library path.png

Be default, only administrator would be able to install packages to the C:/Program Files/ directory, so you need to set permissions for that R library directory to current windows user, or to all users.

Full control RLib.png


After that, the core R packages would be able to be installed or updated.


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