Hi everyone,
I'm a complete beginner when it comes to genetic association analysis. In our homework we have a database that only contains 500 SNPs all centered 300kb around the PITX2 gene on chromosome 4. I had to do a logistic regression in Plink and then need to make a manhattan plot of the results from my.assoc output file.
Now, I've never been good with Excel, so I tried every possible way and I never seem to get it right, it also doesn't seem to be the most common way to do it. My teacher said we could do it by manipulating a scatterplot but I'm unable to get satisfying results.
I heard about Locuszoom but the old version doesn't take on build GRCh38 and the new version which does seems not to be able to take a plink output since it's space-delimited rather than tab-delimited. Is there a way to bypass this, or modify my output from Plink to be tab-delimited?
Lastly I've tried with R with the qqman library, but now my problem is that I don't think I can choose a specific 300kb around a gene, the most I can do is choose a single Chromosome, so my manhattan plot is basically just a vertical line.
So now, I'm wondering if there's an easy way to do this that I'm missing in either of the 3 methods or even another simple method.
Thanks in advance for your help!
You can check LDLink website for specific region plotting