MicroArrayRunRScript.pdf

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Run RScript (Microarray Data)

Overview

The Run RScript (Microarray Data) command allows the user to run an R-script, based on a dataset in the Solution Explorer. The data is sent out to R, the script is run, and any results from R are imported back into Array Studio as a Table object.

To run this module, type MicroArray | R | Run R Script(Microarray Data).

R menu.png

Input Data Requirements

This module works on -Omic data types.

General Options

RunRScipt0.png

Input/Output

  • Project & Data: The window includes a dropdown box to select the Project and Data object to be filtered.
  • Variables: Selections can be made on which variables should be included in the filtering (options include All variables, Selected variables, Visible variables, and Customized variables (select any pre-generated Lists)).
  • Observations: Selections can be made on which observations should be included in the filtering (options include All observations, Selected observations, Visible observations, and Customized observations (select any pre-generated Lists).
  • Output name: The user can choose to name the output data object.


Options

  • Choose a script to run: The user must first choose the script to run. Scripts must be kept in the user’s (OmicsoftDirectory)\Pipeline\RScripts\MicroArray folder.
    • View Script: This will open the content of the selected R script in a text file.
    • Download Script: Clicking this link will allow users to download an R script from Omicsoft's server.
  • Input parameters (one per line): Once the script is loaded(selected), this window will automatically load the R script and show the parameter.
  • Output dataframe names: The output dataframe names will automatically show up when the user selects the script. Please do not modify the output names, as they are keys for Array studio to communicate with R. Note that in this case, the Output name in Input/Output section is not used.
Tips.pngR Integration shows how to write a R script for Array studio to load and run.


Output Results

For each data frame generated by the R script, a new Table data object will be generated project's folder in the Solution Explorer.

OmicScript

Run R Script


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