Using this software0. For impatient users
1. Data inputs
2. Create a project
3. Annotate a project
Using user annotation track
4. Filter for quality scores
5. Main user interface
6. SVA genome browser
7. SVA tables
8. Selecting genes or regions
Bio-pathway or GO
Fisher's exact test
10. Exome or targeted capture sequencing
Using SVA Analysis functions - Fisher's exact test
SVA implements the Fisher's exact test as one way to examine the association between genetic variants and the target trait or disease of interest.
Requirement of this test
This function requires the case/control status is specified in the pedinf file, which is an optional input file for an SVA project. This file can be specified using this statement in the SVA project file: '[PEDINFO]='. Here is the description and example of of this file.
This function also assumes that the studied subjects are not biologically related, i.e., although the pedinf file itself is in a linkage format, no members from the same family should be included in this test.
Performing this test
To access the Fisher's exact test function, go to the menu “Analysis ->Fisher's exact test '.
Then you will be asked to specify the output file. Five genetic models will be tested:
The results for each model will be outputted to a separate file. For example, if you specify the output file as 'MyFisherTest', the output files will be:
There are 7 columns in the output file:
Each result file is ordered by column 7, the P value, in an ascending order. Here is an example of the output file:
How this test is performed
SVA prepares the variant data in linkage formats and uses an independent software tool, PLINK, to perform the Fisher's exact test. PLINK is a software tool authored by Shaun Purcell at the Center for Human Genetic Research , Massachusetts General Hospital, and the Broad Institute of Harvard & MIT. SVA user does not need to download and install PLINK separately.
© 2011 Dongliang Ge, PhD.