Hello,
I am working on beta-thalassemia, where I am comparing two different groups based on their phenotype using targeted NGS. I have used the tools HaploView and PLINK to compare these two groups. By using HaploView, I have got a few tagged SNPs by comparing these groups. Now I want to study if there is any association between these SNPs with the phenotype of the two groups.
Can anyone suggest the type of statistics I can use in this study?
Thanks
As far as I am concerned, a test like Chi-square or Fisher's Exact test can be used to assess the level of association between two (or more) categorical variables like the defined groups and genotype frequency. There is a bunch of software that you can use for this purpose like plink or some R packages like SNPassoc ...
If you provide more details, you might get a more detailed answer.
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