Plotting SNPs with different allele frequency between population

Question

[seta]

Hi all,

I have a set of SNPs (about 2000 snps) related to a given trait, which their allele frequencies are significantly different between two populations of under study. Could you please suggest me how I can plot these SNPs in an appropriate way?

Thanks in advance

Answer 1

[Kevin Blighe]

Plot all p-values from your tests as negative log (base 10) of the p-value, as in a Manhattan Plot. You can use qqman package in R (on CRAN).

Kevin

[seta]

Thanks Kevin, besides p-value, I have also odds ratio (OR) that show the difference level, here. Is it needed to show it, too, in your view? if yes, could you please kindly let me know how I can show both, the p-value and OR in the same graph?

[Kevin Blighe]

For the ORs, you should consider a Forest Plot: https://cran.r-project.org/web/packages/forestplot/vignettes/forestplot.html

[seta]

So, it is not possible to show both (log.pvalue and OR) in the single graph, yes?

[Kevin Blighe]

It is possible - you just need to be creative and design / plan it. One does not require a pre-existing package/function for everything, of course.