I used qtscore() in GenABEL to do GWAS. But my smaple size is small. Someone suggested me to do bootstraps without replacement
and gave me a formula (A)
A:
Code: Select all
qtscore(sample(phdata(b.dat)$disease), replace=F), b.dat, trait ="binomial")but I think this formula is wrong, because it only sampled phentypes but without relevant genotype information.
I think the right formular is (B)
B:
Code: Select all
qtscore(disease, b.dat,trait ="binomial", idsubset=sample(gtdata(b.dat)@idnames,replace=F),times=1000)am I right? or anyother good suggestions?
I also have a question:
what's the meaning of "times" in qtscore(), if times=1000, does it mean that in my formula the sample process run 1000 times?
if times=1000, what's the meaning of P1df in results? How can I calculate FDR(false discovery rate)?
Thank you!