Question: Any Recommendation On Program That Could Simulate Gwa Case/Control Data ?
5
gravatar for Tg
8.9 years ago by
Tg310
Thailand
Tg310 wrote:

Hi, I wonder is program for simulate a gwa case/control data with LD pattern intact ( I want to use LD pattern from CEU hapmap). I want to simulate genotype for illumina/affymetrix chip.

From what I googling, I found gwasimulator (http://biostat.mc.vanderbilt.edu/wiki/Main/GWAsimulator) and plink. Are these two ok for a jobs ? Or there's any better alternative ?

thanks

linkage gwas simulation data • 4.7k views
ADD COMMENTlink modified 8.8 years ago by Larry_Parnell16k • written 8.9 years ago by Tg310
1

Would permutation testing of the hapmap data work for your purpose. If the reason for simulation is to generate empirical p-values, then PLINK may work. http://pngu.mgh.harvard.edu/~purcell/plink/perm.shtml

ADD REPLYlink written 8.9 years ago by jvijai1.1k
4
gravatar for Genotepes
8.7 years ago by
Genotepes950
Nantes (France)
Genotepes950 wrote:

Hi

GenomeSimla si doing OK. HapGen is not too bas neither and may require slightly less involvment and time to understand the parameters.

Disclaimer : didn't work on any of these program but used them both.

ADD COMMENTlink written 8.7 years ago by Genotepes950
3
gravatar for Stephen
8.8 years ago by
Stephen2.7k
Charlottesville Virginia
Stephen2.7k wrote:

Take a look at genomeSIMLA, also from Vanderbilt. Disclaimer: I worked on this project for a time when I was at Vanderbilt. It uses a forward-time approach with Hardy-Weinberg principles to generate LD. You can embed a disease model to simulate case-control outcomes, or simulate quantitative traits, including gene-gene interaction. The developer working on genomeSIMLA, Eric, is pretty prompt about answering questions or troubleshooting. Give it a try.

http://chgr.mc.vanderbilt.edu/genomeSIMLA/

ADD COMMENTlink written 8.8 years ago by Stephen2.7k
2
gravatar for Larry_Parnell
8.9 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

We do not do such here. We'd prefer to use real data. In that regard, I suggest you look at the GWAS data available from the Wellcome Trust Consortium.

I know some people who use PLINK but have never heard of them using it for the purpose you propose.

Added in edit 20 Sep 2011: There is a timely paper from the Butte group at Stanford using the available Wellcome Trust data to show that when one examines GWAS data by sex, there are important findings with respect to sex differences and disease risk. Take a look at the paper for details on analyzing data (genotypes) generated by another group.

ADD COMMENTlink modified 8.2 years ago • written 8.9 years ago by Larry_Parnell16k

Would doing a permutation testing of the Hapmap data work for you? PLINK can do that.

ADD REPLYlink written 8.9 years ago by jvijai1.1k

Well, I just skim on it, didn't really go into detail on plink.

I do have some GWAS data (not wtccc one though) but I'm looking for some way to validate my analysis beside testing with real data.

ADD REPLYlink written 8.9 years ago by Tg310
2
gravatar for 0Asa
8.2 years ago by
0Asa20
Belgium
0Asa20 wrote:

Note that there are also these:

Haven't used any of them yet but planning to.

Also, I just asked a similar question right here.

ADD COMMENTlink modified 12 weeks ago by RamRS25k • written 8.2 years ago by 0Asa20
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