[R] scrime Package simulatedSNP function

From: Claire_6700 <chriseverclear_at_hotmail.com>
Date: Thu, 08 May 2008 16:41:18 -0700 (PDT)

Hello,

I need some help with the simulatedSNPs function from scrime package.

I am trying to simulate some genotype of a case/control disease locus. The allele frequence are cases/controls

Sample     cases      controls
2000         .5            .10
1500         .6            .40

In each of the row, i need to simulate 100 snp and calculate the pvalue

##############Download Scrime Package###########################
library(scrime)
n.obs<-1000
n.snp<-100
vec.ia<-1
simulateSNPs(n.obs, n.snp, vec.ia, prop.explain = 1,
list.ia.val = NULL, vec.ia.num = NULL, maf = c(0.1, 0.12),
prob.val = rep(1/3, 3), list.equal = NULL, prob.equal = 0.8,
rm.redundancy = TRUE, shuffle = FALSE, shuffle.obs = FALSE, rand = NA)

What is the right parameter. I am pretty new with R.

wrong result.
  Interaction Cases Controls
1 SNP1 == 2 500 0 any help will be appreciated.

thanks
Claire

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