Question: Plotting SNPs with different allele frequency between population
0
gravatar for seta
12 months ago by
seta1.2k
Sweden
seta1.2k wrote:

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

snp population plotting • 582 views
ADD COMMENTlink modified 12 months ago by Kevin Blighe52k • written 12 months ago by seta1.2k
0
gravatar for Kevin Blighe
12 months ago by
Kevin Blighe52k
Kevin Blighe52k wrote:

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

ADD COMMENTlink written 12 months ago by Kevin Blighe52k

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?

ADD REPLYlink modified 12 months ago • written 12 months ago by seta1.2k

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

ADD REPLYlink written 12 months ago by Kevin Blighe52k

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

ADD REPLYlink written 12 months ago by seta1.2k

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.

ADD REPLYlink written 12 months ago by Kevin Blighe52k
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