Rare variant association analysis (SKAT-O)

Hello everyone,

I was wondering if it is statistically acceptable to perform SKAT-O analysis one a single gene.

To elaborate, I am looking in a miRNA gene (80nt length) and I have found a small number of rare variants present in my case group, but none in my control group. Running SKAT-O for adjusted sample size (case+control = 1700 <2000) I get a p.value <0.05.

I was wondering though, is this realistic? I have been trying to make a power calculation in the P-SKAT framework in R but I have been experiencing issues due to subregion.Length, I think.

out.b<-Power_Logistic(SubRegion.Length=100, Causal.Percent=40, alpha=0.05, N.Sim=100 , MaxOR=3, Negative.Percent=20)

On one hand, I am thinking since I am not getting any errors/warnings and I reach a significant p.value, that I should not worry. On the other hand, I am still a bit sceptical.

Any feedback welcome, including any alterations in the code I am using for power calculation (maybe I should eventually include matrices with Haplotypes and SNP.Location?).

Thanks in advance,
Alex

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