http://genome.sph.umich.edu/w/index.php?title=RareSimu&feed=atom&action=historyRareSimu - Revision history2024-03-28T09:55:33ZRevision history for this page on the wikiMediaWiki 1.35.9http://genome.sph.umich.edu/w/index.php?title=RareSimu&diff=14615&oldid=prevPpwhite: /* Download */2017-02-02T15:11:59Z<p><span dir="auto"><span class="autocomment">Download</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:11, 2 February 2017</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Download ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Download ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The current version is available for download from http://<del class="diffchange diffchange-inline">www</del>.sph.umich.edu/<del class="diffchange diffchange-inline">csg</del>/weich/GMS.tar.gz</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The current version is available for download from http://<ins class="diffchange diffchange-inline">csg</ins>.sph.umich.edu//weich/GMS.tar.gz</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== TODO ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== TODO ==</div></td></tr>
</table>Ppwhitehttp://genome.sph.umich.edu/w/index.php?title=RareSimu&diff=11386&oldid=prevWeich: Created page with "Genetic Model-based Simulator [GMS] is an efficient c++ program for simulating case control data sets based on genetic models. The input is a pool of haplotypes and a text fil..."2014-08-28T03:28:50Z<p>Created page with "Genetic Model-based Simulator [GMS] is an efficient c++ program for simulating case control data sets based on genetic models. The input is a pool of haplotypes and a text fil..."</p>
<p><b>New page</b></p><div>Genetic Model-based Simulator [GMS] is an efficient c++ program for simulating case control data sets based on genetic models. The input is a pool of haplotypes and a text file for model specification. <br />
The output is a set of simulated datasets in the format of Merlin ped file. <br />
<br />
== Basic Usage Example ==<br />
<br />
In a typical command line, a few options need to be specified together with the input files. <br />
Here is an example of how GMS works:<br />
<br />
./GMS --hapfile test.hap --snplist test.lst --model model.heter.txt --f0 0.01 --<br />
nrep 100 --ncase 250 --nctrl 250 --causal --prefix tmp<br />
<br />
== Command Line Options ==<br />
<br />
=== Basic Output Options ===<br />
<br />
--hapfile a pool of simulated or real haplotypes, one chromosome per row<br />
--snplist snp names in the order ofhaplotypes in hapfile, one snp per row<br />
--model a model file specifying genetic models, see below for details<br />
--nrep the number of replications<br />
--seed seed for random number generator<br />
--ncase the number of cases in each replicate<br />
--nctrl the number of controls in each replicate<br />
--f0 overall baseline prevalence<br />
--prefix prefix of output files (e.g. prefix.rep1.ped, prefix.rep2.ped)<br />
--causal only generate causal SNPs in the output pedigree file<br />
<br />
<br />
=== Model File Annotation ===<br />
The model file includes one header line and multiple rows after. Each row responding to a set of <br />
SNPs with desired frequency range and relate risk (RR) or odds ratio (OR)<br />
<br />
1. Heterogeneity Model<br />
<br />
a) COUNT FREQ_MIN FREQ_MAX RR1 RR2<br />
<br />
b) FRACTION FREQ_MIN FREQ_MAX RR1 RR2<br />
<br />
2. Logistic Model<br />
<br />
a) COUNT FREQ_MIN FREQ_MAX OR1 OR2<br />
<br />
b) FRACTION FREQ_MIN FREQ_MAX OR1 OR2<br />
<br />
== How It Works ==<br />
There are two underlying models. Disease status follows a Bernoulli distribution with P <br />
<br />
1. Heterogeneity Model<br />
<math> P(D | (AA,AA,...,AA)) = f_0 </math><br />
<br />
<math> P = \sum_{i=1}^N P(D|x_i) </math><br />
<br />
<br />
2. Logistic Model<br />
<br />
<math>logit(y) = \beta_0 + \sum_{i=1}^{N}\beta_i\times x_i</math><br />
<br />
<math> P = \frac{e^{\beta_0 + \sum_{i=1}^{N}\beta_i\times x_i}}{1+e^{\beta_0 + \sum_{i=1}^{N}\beta_i\times x_i}}</math><br />
<br />
== Download ==<br />
<br />
The current version is available for download from http://www.sph.umich.edu/csg/weich/GMS.tar.gz<br />
<br />
== TODO ==<br />
1. Support Quantitative trait.<br />
<br />
2. Support family structures.<br />
<br />
3. Support more "reasonable" models.</div>Weich