PING automation scripts

This is a set of scripts to use with the Pediatric Imaging, Neurocognition, and Genetics (PING) study. Please see http://pingstudy.ucsd.edu/ for more information about this study.

Installation

All installation dependencies are defined in the requirements.txt file.

Installation steps:

1. git clone git@github.com:guruucsd/PING.git
2. cd PING
3. sudo pip install -r requirements.txt If this fails:
   • Make sure you have pip installed: https://pip.pypa.io/en/latest/installing.html
   • If it fails installing numpy or scipy, I suggest installing miniconda and installing them via conda install numpy scipy pip
4. Visit https://ping-dataportal.ucsd.edu/applications/User/requestLogin.php and request access to the PING data portal.

Scripts

The following functions of the data portal are available through this scripting interface:

• export.py - Compute some derived measures from the PING data, and export to a local CSV
• grouping.py - Plot regressions, separating data by the chosen groupings.
• gwas.py - PRELIMINARY--you must request access before using! download GWAS results, or launch a new GWAS study.
• scatter.py - Show scatter plots, filtering columns by prefix and choosing computations for x, y, and point size.
• similarity.py - Script interface for viewing similarity matrices between different PING measures. Select measures by prefix, and use correlation or partial correlation.
• snps.py - Script interface for the SNP browser; find genes associated with SNPs, SNPs associated with genes, and download user data for specific genes. NOTE: PING limits SNP downloads to 5000, so use them wisely!
• upload.py - Upload your local CSV with derived measures to the PING data portal, so you can access in the Data browser.

Authenticating in scripts

Scripts must be run with a valid username and password to the PING portal--if you don't have one, you'll need to request one.

There are two ways to pass your username and password to the scripts:

• Via the command-line: use parameters --username=[USERNAME] --password=[PASSWORD]
• Via the shell: set the following environment variables:
  • PING_USERNAME - your PING data portal username (not your email address).
  • PING_PASSWORD - your PING data portal password

Example script usage

These examples assume that you've set your username and password via shell environment variables. If you haven't, you'll need to add the --username=[USERNAME] and --password=[PASSWORD] options to the commands below.

• python export.py - exports data sheet, including computed measures, to a local CSV file.
• python grouping.py MRI_cort_area.ctx Gender - show linear regression for each cortical area measure, with regression by gender overlaid on the same plot.
• python scatter.py MRI_cort_area AI:mean AI:std LH_PLUS_RH:mean - show a scatter plot over cortical area measures, of asymmetry index mean vs. standard deviation, with dot size given by the total area (LH+RH)
• python similarity.py MRI_cort_area partial-correlation "Left Hemisphere" - show a similarity matrix between all measures with the MRI_cort_area prefix, using partial correlation, for the left hemisphere only.
• python snps.py view STK31 - show all SNPs associated with gene STK31, according to the PING genetics DB.