sample() in qtscore() of GenABEL

Question

[snowy]

Hello, I used qtscore() in GenABEL to do GWAS. As my sample size is small, someone suggested me to do bootstraps without replacement and gave me a formula (A)

A: qtscore(sample(phdata(b.dat)$disease, replace=F), b.dat, trait ="binomial")

but I think this formula is wrong, because it only sampled phenptypes but without relevant genotype information.

I think the right formula is (B):

B: qtsocre(disease, b.dat, trait="binomial", idsubset=sample(gtdata(b.dat)@idnames, replace=F), times=1000)

Am I right? Or any other 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)?