ANOVA with Phenotype and SNPs
Author: Autumn Laughbaum, Golden Helix, Inc.
This function makes use of the scipy package, specifically the scipy.stats.f_oneway and scipy.stats.kruskal functions. This requires a numeric phenotype column and several genotype columns which provide the grouping structure in each test. Including missings as a group is optional.
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.