I am looking for the best software used today to do eQTL analysis (the association of SNPs genotyped using a chip with genome-wide expression levels), and an updated step-by-step tutorial that could guide me. I am having trouble keeping up with all the different r packages that keep getting updated. I would like to use snpMatrix which is included now in snpStats, or GGtools which seems like a very nice package, but I am finding it very confusing to understand since it is tied to other packages (like snpmatrix) for the input and initial steps. There are great tutorials for GGtools describing what to do once the data is already inputed in this format, but I can't find a good tutorial which describes the steps from the start.
I am not sure whether there is any detailed tutorial which outlines for example:
- Input file description
- association of Snps and expression (i.e. expression as outcome)
- Find cis eQTL (within for example 1 Mb of start/stop site of all the genes) and trans eQTL, and 4. p-value adjustements using permutation and Bonferroni.
If such a tutorial does not exist, could you please point me to the most updated tutorial, if there is one, which apply to the current versions of these softwares?
Any help is very appreciated. Thank you very much.