5  Simulation

The simulation module generated files for marker genotypes and trait values that are to be used in QTL analysis.

Follow the steps below to generate simulation data:

 

è Step 1: Click “Simulation” on the main window and a pull-down menu will show up

è Step 2: Click “Setting parameter” and a dialog window will pop up where you set parameters for your simulation

è Step 3: Click “OK” to accept all parameters that you have set for your simulation.

è Step 4: Repeat step 1 to activate the pull-down menu.

è Step 5: Click “Go simulation” and a new window will appear showing descriptive results of simulation.

è Step 6: When the simulation is done, close the simulation window.

 

5.1 Setting parameters

 

Steps 1 through 3 set parameters for simulation in a dialogue window, which is discussed in details below.

 

~[OK]  Accept all parameters and quit the “Set parameters for simulation” dialogue

~[Cancel]  Discard all parameters and quit the “Set parameters for simulation” dialogue

~[Use default]  Use default parameters for simulation

~[Set as default]   Set your own default parameters which can be used repeatedly.

Distributed with the package, simu_Al.def provides a set of default parameters for simulation.

 

Input files and pedigree type:

~[Genome info]  Input the name of file for genome information. By the default, the file name is given as “genome.txt”. If you have the file in a folder elsewhere, use browse button at the right side to search for it.

~[Pedigree file]  Input the name of the pedigree file. By the default, the file name is given as “pedigree.txt”. If you have the file in a folder elsewhere, use browse button at the right side to search for it.

~[Progeny type]  Choose type of inbred crosses. Currently, this subroutine simulated QTL mapping data for BC1 (backcross to paternal parent), BC2 (backcross to maternal parent), F2 (intercross of F1), and DHL (double haploid lines).

Output files:

~[f1 par markers]  Input the name of file for F1 marker genotypes. By the default, the file name is given as “f1.txt”. If you have the file in a folder elsewhere, use browse button at the right side to search for it.

~[Progeny markers]  Input the name of file for marker genotypes of all progeny. By the default, the file name is given as “markers.txt”. If you have the file in a folder elsewhere, use browse button at the right side to search for it.

~[Quantitative trait]  Input the name of file for trait values of all progeny. By the default, the file name is given as “pheno.txt”. If you have the file in a folder elsewhere, use browse button at the right side to search for it.

~[Save log files for simulation data]  Check this option if you want to save additional simulation data to files. By default, these files are:

~logAV.txt      This is a text file that contains simulated allele values of QTL.

~logPAV.txt   This is a text file that contains simulated QTL allele configuration in all parents.

~logErr.txt      This is a text file that contains residual values of all progeny.

 

General information:

~[Total chromosomes]   How many chromosomes are involved in your QTL mapping analysis?

~[Total number of QTL]  How many QTL are to be simulated on these chromosomes?

~[Total QTL heritability]  Enter total percent variance contributions of all QTL. This value serves as a maximum bound to the sum of percent additive variance of all simulated QTL.

~[Random seed]  This number is used as the seed for generating random numbers.

~[Random sample QTL allele]  Check this option if you need to randomly sample QTL alleles for parents from a given gene pool. If this option is turned on, the number of alleles actually present in parents does not necessarily equal to the number of alleles that you specify in simulation settings.

~[Set allele values in file]  Check this option if allele values are given in a file. If this option is checked true, you’ll need to give the name of file in the edit box below. If you have the file in a folder elsewhere, use the browse button at the right side to search for it. Refer to Section 5.2 for the file format.

~[Set allele configuration in file]  Check this option if allele configurations are given in a file. If this option is checked true, you’ll need to give the name of file in the edit box below. If you have the file in a folder elsewhere, use the browse button at the right side to search for it. Refer to Section 5.2 for the file format.

 

Single chromosome:

èThe number of chromosomes must be given before you work on setting for each chromosome. Entries for each chromosome include:

~ [Current chr]  no of current chromosome that you are working on.

~ [Linkage length, cM]  the linkage length in cM of the current chromosome.

~ [Number of markers]  how many markers are located on the current chromosome.

When 2 or more chromosomes are involved, use the following buttons to navigate these chromosomes:

~[|<<]  Go to first chromosome

~[<<]   Go to previous chromosome

~[>>]   Go to next chromosome

~[>>|]  Go to last chromosome

Caution: you need to press “confirm” button to accept entries for each chromosome. Once you change the number of chromosome, settings for each chromosome become invalid. You’ll have to re-enter and re-confirm settings for each chromosome.

 

Single QTL:

èThe number of QTL must be given before you work on setting for each QTL. Entries for each QTL include:

~ [Current QTL]  no of current QTL

~ [on chromosome]  which chromosome the QTL is assumed to be on

~ [position, cM ]  chromosomal location of the current QTL.

~ [allele number]  allele number of the current QTL

~ [additive variance]  additive variance of the current QTL

Use the following buttons to navigate these QTL:

~[|<<]  Go to first QTL

~[<<]   Go to previous QTL

~[>>]   Go to next QTL

~[>>|]  Go to last QTL

Caution: you need to press “confirm” button to accept entries for each QTL. Once you change the number of QTL, settings for each QTL become invalid. You’ll have to re-enter and re-confirm settings for each QTL.

 

5.2 Files for allele values and configurations

 

Sometimes, you may need to run the analysis with known QTL effect or/and configuration. This can be done by providing them in files.  Next are examples that you can follow when you prepare these files.

 

5.2.1 Allele value file

 

This is a text file that contains allele values for all QTL. The following is example file that contains allele values for 6 QTL, where the number of alleles at each QTL is 10, 4, 2, 3, 6, and 5, respectively. ATTENTION: words in { } are comments and they should not be include in the file.

 

  {allele values for the first QTL}

  QTL_0_Al_0       -0.1493    {1st allele value}

  QTL_0_Al_1        0.2781    {2nd allele value}

  QTL_0_Al_2        0.0525    {3rd allele value}

  QTL_0_Al_3        0.2752    {4th allele value}

  QTL_0_Al_4       -0.3634    {5th allele value}

  QTL_0_Al_5        0.1985    {6th allele value}

  QTL_0_Al_6       -0.3236    {7th allele value}

  QTL_0_Al_7        0.0061    {8th allele value}

  QTL_0_Al_8        0.2823    {9th allele value}

  QTL_0_Al_9       -0.2564    {10th allele value}

 

  {allele values for the second QTL}

  QTL_1_Al_0        0.16      {1st allele value}

  QTL_1_Al_1        0.2307    {2nd allele value}

  QTL_1_Al_2       -0.084     {3rd allele value}

  QTL_1_Al_3       -0.3067    {4th allele value}

 

  {allele values for the third QTL}

  QTL_2_Al_0       -0.2121    {1st allele value}

  QTL_2_Al_1        0.2121    {2nd allele value}

 

  {allele values for the fourth QTL}

  QTL_3_Al_0        0.0874    {1st allele value}

  QTL_3_Al_1       -0.2418    {2nd allele value}

  QTL_3_Al_2        0.1544    {3rd allele value}

 

  {allele values for the fifth QTL}

  QTL_4_Al_0        0.1925    {1st allele  value}

  QTL_4_Al_1        0.2543    {2nd allele value}

  QTL_4_Al_2       -0.1675    {3rd allele value}

  QTL_4_Al_3       -0.0584    {4th allele value}

  QTL_4_Al_4        -0.216     {5th allele value}

  QTL_4_Al_5       -0.0048    {6th allele value}

 

  {allele values for the six QTL}

  QTL_5_Al_0         0.451    {1st allele value}

  QTL_5_Al_1       -0.2255   {2nd allele value}

  QTL_5_Al_2        0.1933   {3rd allele value}

  QTL_5_Al_3       -0.0216   {4th allele value}

  QTL_5_Al_4       -0.3972   {5th allele value}

 

5.2.2 Allele configuration file

 

This is a text file that contains allele configuration of all QTL that are present in 5 founder parents. The following is example file that set allele configuration for the above 6 QTL. One may notice that the number of alleles actually segregating is less that the true of QTL alleles that we have preset, and this is allowed in the analysis using INTERQTL. ATTENTION: words in { } are comments and they should not be include in the trait file. 

 

        {Set allele configuration parent by parent. Allele no corresponds to that given in allele value file }

        Par_0       2     0     1     2     4     1    {alleles carried by parent 0 at QTL 0, 1, 2, 3, 4, and 5 }

        Par_1       2     0     0     2     4     4    {alleles carried by parent 1 at QTL 0, 1, 2, 3, 4, and 5 }

        Par_2       4     2     0     2     0     1    {alleles carried by parent 2 at QTL 0, 1, 2, 3, 4, and 5 }

        Par_3       4     3     0     2     3     0    {alleles carried by parent 3 at QTL 0, 1, 2, 3, 4, and 5 }

        Par_4       8     0     1     1     1     1    {alleles carried by parent 4 at QTL 0, 1, 2, 3, 4, and 5 }