Re: [R] genotypes simulation

From: Claire_6700 <>
Date: Mon, 05 May 2008 16:25:43 -0700 (PDT)

thank you. i will take a look


Neil Shephard wrote:
> Claire_6700 wrote:

>> Hello,
>> I am having really hard time finding a good article about simulating
>> genotypes of cases and controls at a disease locus using R.
>> if you guys can point me or guide me where i can find more information,
>> it will be helpful.

> The popgen() package allows the simulation of genotype data under a
> coalescent model (via the treesim() function) or Multinomial-Drichlet
> model (via the simMD() function). These won't quite simulate case-control
> data, but can no doubt be tweaked to get two sets of data (cases and
> controls) with the desired allele frequencies, LD etc.
> There is also the rmetasim() package which interfaces R with metasim.
> Alternatively if your after validation of p-values derived from genotypic
> tests of association via simulation there is also the Direction Simulation
> Approach (DSA) which is implemented in R
> (
> There is also an R plugin for plink
> ( which performs simulation of
> unlinked loci that are in linkage equilibrium (although you may
> specifically want to model linkage disequilibrium).
> And there is an R-plugin for PBAT which is for Population Based
> Association Tests (
> For other R-genetics information you may find the task-view at
> useful as well as
> There are also a host of other non-R options available though. Many under
> the coalescent model (including one of the first by Richard Hudson, the ms
> program) are linked from
> and additional
> software for genetic analysis (including simulation in some instances) at
> . The vast majority will simply dump
> output to text files, so its straight-forward to call them from within R
> via a system call and then read the results into R.
> Neil
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