Question: How to calculate the p-value of frequency of my study and control of some variants?
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gravatar for mullin.yu
4 weeks ago by
mullin.yu0
mullin.yu0 wrote:

Dear all,

I'm not good at statistics, which method will be preferred? Fisher's exact test or Chi Square test with Yates' continuity correction? Any R code can be shared?

Data file (say 1000G_EAS is the frequency from 1000 Genome project of EAS population):

variant,this_study,1000G_EAS
rs9934438,0.916,0.885
rs2228001,0.836,0667
rs10655852,0.821,0.571
rs4244285,0.429,0.313
rs3745274,0.402,0.215
rs2108622,0.394,0.214

Thanks a lot!

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by mullin.yu0

Fisher exact test, but with allele counts, not frequencies

ADD REPLYlink written 4 weeks ago by WouterDeCoster42k
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