KBAC with Permutation Testing
Author: James Grover, Golden Helix, Inc.
The Kernel-Based Adaptive Cluster (KBAC) method by Liu and Leal [Liu and Leal 2010] first catalogs the variant data within each of a number of regions into multi-marker genotypes. Since the variants are rare, only a relatively few different multi-marker genotypes will be found in any given region.
Recommended Directory Location
Save the script to the following directory:
*..\Application Data\Golden Helix SVS\UserScripts\Spreadsheet\Analysis
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 Analysis menu.
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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.