I am sort of new in the field. I want to know two things
If someone has worked with PLINK for association studies in bacteria. The chase is that I have a gene presence/absence table and want to assess if one of those genes is significantly related to a particular phenotype. Is this possible with PLINK? I actually saw someone do it and I would like to understand the rationale behind the formatting of the .ped and .map files as well as the analysis.
As far as I remember, the affected (case) and unaffected (control) groups are my bacterial phenotypes, but there's more than that. I think there are some columns to add to those files.
If someone has more experience, please let me know.
Not sure if this is the appropriate place to ask this. If not, my apologies.