[R] Simulation Case/Control R Beginner

[Claire_6700]

I am looking for a way to simulate genotypes of cases and control at a
disease locus in R. I am supposed to set the allele frequency as
control/cases. for each of the column below simulate 200 snp dataset.

I am looking at treesim function from popgen to stimulate the genotypes in
R.

Here is what i have

size         case   control 
2000        0.6        0.15
2500        0.1        0.17

what am i missing in the treesim parameter and how do i calculate the
p-value of trend test?

I am a bit confused with the parameter. 

N<-2000
Sn<-200
theta<-0

a<-treesim(N, Sn, theta, rho.vec, mutations=FALSE, sample=FALSE)
mat<-LDmat(.....)


Here is the documentation.
http://cran.r-project.org/web/packages/popgen/popgen.pdf

any help will really be helpful.

thank you,
Claire
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