LD Score Regression
Author: Alison Figueira, Golden Helix, Inc.
Calculates heritability scores, genetic correlation, and genetic covariance using the ldscore module (installed separately)
Step 1: Install the Python Script
Save the script to the following directory:
*..\Application Data\Golden Helix SVS\UserScripts\Spreadsheet\Genotype
Note: The Application Data folder is a hidden folder on many operating systems and its location varies between operating systems. The easiest way to locate this directory on your computer is to open SVS and go to Tools > Open Folder > UserScripts Folder. If saved to the proper folder, this script will be accessible from the Spreadsheet Genotype menu.
Step 2: Install the ldscore Module
Download the ldscore.zip file and extract the folder named ldscore
Copy or move the folder to the SVS Install directory under the Lib\stats sub-folder
Note: You can navigate to the SVS install location by going to Tools > Open Folder > SVS Install Folder.
Need a Custom Script?
Need a script and don't feel you have the bioinformatics expertise to write it yourself? Click the link below to request a custom script and we'll see what we can do to help.
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What is Python?
Python is a clear and powerful object-oriented programming language, comparable to Perl, Ruby, Scheme, or Java. Integrating Python into SVS provides full programmatic access to many of the software's features enabling the augmentation of existing tools, creating entirely new ones, automation of work flows, integration with other programs and more.