Closed holtzy closed 6 years ago
Hi! holtzy,
Thanks very much for your using of CMplot! :rose: Actually, CMplot could only visualize the data that share the common SNPs with different p-values. If there is a NA for the SNP, it would be deleted whatever it has p-value for other traits. So i suggest that after merge the 3 GWAS results, you could try to replace NAs with value 1 for the non-common SNPs, then plot it with CMplot. Also i will update the codes to meet your problem. Hope it can solve your problem!
Thanks again!
Lilin
Thanks for your answer and the hint! Yan
First of all, thanks for this nice package
I'm trying to output a stacked Manhattan plot with 3 GWAS summary statistics that have very few SNPs in common (
CMplot
function). It looks like only the SNPs that are common to the 3 dataset are plotted.I am missing something? Or is it possible to improve the code to show all SNPs?
Thank you !