How to calculate the p-value of frequency of my study and control of some variants?
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2.0 years ago
mullin.yu • 0

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!

SNP p-value allele frequency • 460 views
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Fisher exact test, but with allele counts, not frequencies