Question: Plotting SNPs with different allele frequency between population
0
gravatar for seta
16 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 • 725 views
ADD COMMENTlink modified 16 months ago by Kevin Blighe56k • written 16 months ago by seta1.2k
0
gravatar for Kevin Blighe
16 months ago by
Kevin Blighe56k
Kevin Blighe56k 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 16 months ago by Kevin Blighe56k

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 16 months ago • written 16 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 16 months ago by Kevin Blighe56k

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

ADD REPLYlink written 16 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 16 months ago by Kevin Blighe56k
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