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z deprecated GUI Tutorial

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Hae Kyung Im edited this page Jul 28, 2020 · 1 revision

Deprecation warning

This UI is no longer maintained and possibly broken.

Introduction

MetaXcan provides a desktop GUI for convenience and ease of use. This is an example of how to get it set up and running, and is a parallel of the Command Line Tutorial. In this example you might need to run a simple script or two from the command line.

Prerequisites

  • A desktop environment with Tkinter bindings (pretty much covered in Windows and Linux)
  • A bash-like environment and wget for data setup
  • [Python 2.7] (https://www.python.org/)
  • numpy
  • scipy
  • MetaXcan repository cloned into a local folder

#Background

MetaXcan's command line might look hostile to a non technical user. We furnished a streamlined version of the MetaXcan process to be accessed from a local desktop GUI app.

Screen Shot

#Get The Sample data

This example runs on specific example data. If you have not done this previously, you can download example data from this place.

As an example, from an UNIX command line:

$ cd MetaXcan/working/software     # or wathever you downloaded MetaXcan Software
$ wget https://s3.amazonaws.com/imlab-open/Data/MetaXcan/sample_data/sample_data.tar.gz
$ tar -xzvpf sample_data.tar.gz

In this case, sample data covers a transcriptome model built from Depressive Genes and Network whole blood samples, and SNP covariance matrices built from Thousand Genomes samples.

Naturally, you don't need to download these files every time you run MetaXcan.

#Run MetaXcan's UI

Run in a command line terminal, at the repository code folder:

$ cd MetaXcan/working/software     # or wathever you downloaded MetaXcan Software
$ ./MetaXcanUI.py

You should see the main screen of the GUI app as in the previous screen shot. The next step is configuring some options for MetaXcan to run.

  • Check "compressed" option at the top. (sample GWAS is compressed)
  • Enter ".*gz" at the "GWAS Filename Pattern" option (the "GWAS" folder is filled with other support files that we want to ignore)
  • Check "Beta" and "PValue" option (SNP's Zscores will be calculated from this columns in the example GWAS file)

The GUI should look like: Filled GUI

  • hit "Run"

When running, the GUI disables all options except for "QUIT", and "Run Button" transforms into a "Stop button", as in: Running GUI

The process should take a couple minutes to complete in a modern pc; once it finishes, the UI reenables itself to allow runs on different data. Note that the bottom GUI are displays a status log with the process' progress.

GUI finished

Note that the GUI creates some intermediate files when performing calculations. If you run again, the GUI will warn you if it finds preexisting intermediate files, and ask you if you want them deleted. This deletion cannot be undone.

Conclusion

This example showed how to run MetaXcan's GUI. For a thorough explanation of how to use it, please check the GUI reference

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