I have a significant SNP from a Genome Wide Association Study and I want to find correlation between change in this SNP between samples and change in gene expression.
I've manually used ANOVA in R which shows that many genes expression are associated with this SNP.
I'm wondering if there is another tool that anyone has used to perform this kind of analysis that would be staightforward to use. "Interval Mapping" seems to be the more accepted method for eQTL finding.
I've been trying to do this in GGtools but find the documentation to be limited which doesn't make life too easy.