sample()and "times" in qtscore()

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snowy
Posts: 2
Joined: Thu Oct 09, 2014 2:43 am

sample()and "times" in qtscore()

Postby snowy » Tue Nov 03, 2015 2:02 am

Hello!
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!
Last edited by lckarssen on Tue Nov 03, 2015 10:13 am, edited 2 times in total.
Reason: Some formatting of code

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